Mercurial > repos > iuc > trinity_analyze_diff_expr
changeset 0:d4128a4e49ca draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,18 @@ +Trinity memory usage +==================== + +As described on the official Trinity website +`FAQ <http://trinityrnaseq.sourceforge.net/trinity_faq.html#ques_comp_resources_required>`_, +trinity requires a large amount of memory to perform the assembly: "roughly +~1G of RAM per 1M reads to be assembled" + +By default, this tool is configured to limit the memory consumption to 30G. +You might need to lower this limit if the machine(s) executing the jobs have less memory available. +If you have a lot of reads to assemble and a machine with enough memory, you can increase it. +In both cases, you can edit the TRINITY_MEM_OPTIONS in the file: + +<tool_dependency_dir>/environment_settings/TRINITY_MEM_OPTIONS/iuc/trinity/<hash_string>/env.sh + +to lower the maximum memory usage to 2G for example: + +TRINITY_MEM_OPTIONS='--max_memory 2G --bflyHeapSpaceMax 2G'
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/analyze_diff_expr.xml Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,179 @@ +<tool id="trinity_analyze_diff_expr" name="Extract and cluster differentially expressed transcripts" version="@WRAPPER_VERSION@.0"> + <description>from a Trinity assembly</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="2.30.0">bioconductor-biobase</requirement> + <requirement type="package" version="2.2.2">bioconductor-qvalue</requirement> + <requirement type="package" version="1.22.0">bioconductor-goseq</requirement> + <requirement type="package" version="3.3.0">bioconductor-go.db</requirement> + </expand> + <expand macro="stdio"/> + <command><![CDATA[ + ## DE results input files must be in the working directory and have suffix .DE_results + #import re + #for $input in $DE_results + ln -s "${input}" "${re.sub('[^\w\-_.]', '_', input.element_identifier)}.DE_results" + && + #end for + + analyze_diff_expr.pl + --matrix "${matrix}" + --samples "${samples}" + -P ${p} + -C ${c} + + #if str( $additional_params.max_DE_genes_per_comparison ): + --max_DE_genes_per_comparison ${additional_params.max_DE_genes_per_comparison} + #end if + + $additional_params.order_columns_by_samples_file + + #if $additional_params.max_genes_clust: + --max_genes_clust ${additional_params.max_genes_clust} + #end if + + #if str( $additional_params.GO_enrichment.examine_GO_enrichment ) == "yes": + --examine_GO_enrichment + --GO_annots "${$additional_params.GO_enrichment.GO_annots}" + --gene_lengths "${$additional_params.GO_enrichment.gene_lengths}" + #end if + + --output results + ]]></command> + <inputs> + <param format="tabular" name="matrix" argument="--matrix" type="data" label="Expression matrix" help="Raw counts matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool"/> + <param format="tabular" name="samples" argument="--samples" type="data" label="Sample description" help="File describing samples and replicates"/> + <param format="tabular" name="DE_results" type="data_collection" collection_type="list" label="Differential expression results"/> + <param name="p" type="float" argument="-P" value="0.001" label="p-value cutoff for FDR"/> + <param name="c" type="float" argument="-C" value="2" label="min abs(log2(a/b)) fold change" help="Default: 2 (meaning 2^(2) or 4-fold"/> + <section name="additional_params" title="Additional Options" expanded="False"> + <param name="max_DE_genes_per_comparison" argument="--max_DE_genes_per_comparison" type="integer" value="" optional="true" label="Maximum differential expression genes per comparison" help="Extract only up to the top number of DE features within each pairwise comparison. This is useful when you have massive numbers of DE features but still want to make useful heatmaps and other plots with more manageable numbers of data points."/> + <param name="order_columns_by_samples_file" argument="--order_columns_by_samples_file" type="boolean" checked="false" truevalue="--order_columns_by_samples_file" falsevalue="" label="Order columns by samples file" help="Instead of clustering samples or replicates hierarchically based on gene expression patterns, order columns according to order in the --samples file."/> + <param name="max_genes_clust" argument="--max_genes_clust" type="integer" value="10000" label="Maximum genes in cluster" help="If more than 10000, heatmaps are not generated, since too time consuming"/> + <conditional name="GO_enrichment"> + <param type="select" name="examine_GO_enrichment" argument="--examine_GO_enrichment" label="Run GO enrichment analysis" help="To examine GO enrichment, you must first run Trinotate and then extract all GO assignments for each gene feature, with the Trinotate script extract_GO_assignments_from_Trinotate_xls.pl"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <param format="tabular" name="GO_annots" argument="--GO_annots" type="data" label="Extracted GO assignments file" help="Generated by the Trinotate script extract_GO_assignments_from_Trinotate_xls.pl. Must have 2 columns: feature_id GO:000001,GO:00002,..."/> + <param format="tabular" name="gene_lengths" argument="--gene_lengths" type="data" label="Gene length file" help="Must have 2 columns: feature_id length"/> + </when> + </conditional> + </section> + </inputs> + <outputs> + <collection name="extracted_DE_genes" type="list" label="${tool.name} on ${on_string}: extracted differentially expressed genes"> + <discover_datasets pattern="(?P<name>.+)\.subset$" ext="tabular" /> + </collection> + <collection name="summary_files" type="list" label="${tool.name} on ${on_string}: summary files"> + <data format="tabular" name="results_matrix" from_work_dir="results.matrix"/> + <data format="tabular" name="results_matrix_log2_centered" from_work_dir="results.matrix.log2.centered.dat"/> + <data format="pdf" name="results_matrix_log2_centered_heatmap" from_work_dir="results.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/> + <data format="tabular" name="results_matrix_log2" from_work_dir="results.matrix.log2.dat"/> + <data format="tabular" name="results_matrix_log2_sample_cor" from_work_dir="results.matrix.log2.sample_cor.dat"/> + <data format="pdf" name="results_matrix_log2_sample_cor_matrix" from_work_dir="results.matrix.log2.sample_cor_matrix.pdf"/> + </collection> + <data format="RData" name="rdata" label="${tool.name} on ${on_string}: RData file" from_work_dir="results.matrix.RData"/> + <collection name="GOseq_enrichment" type="list" label="${tool.name} on ${on_string}: GOseq enriched and depleted categories"> + <discover_datasets pattern="(?P<name>.+\.subset\.GOseq\.(enriched|depleted))$" ext="tabular" /> + </collection> + </outputs> + <tests> + <test> + <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> + <param name="samples" value="count/samples.txt"/> + <param name="DE_results"> + <collection type="list"> + <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results" ftype="tabular" /> + <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" /> + <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" /> + </collection> + </param> + <output_collection name="extracted_DE_genes"> + <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.0.wt_37-UP" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset"/> + <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.0.wt_GSNO-UP" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset"/> + <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_37-UP" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset"/> + <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_ph8-UP" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset"/> + <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_GSNO-UP" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset"/> + <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_ph8-UP" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset"/> + </output_collection> + <output_collection name="summary_files"> + <element name="results_matrix" compare="sim_size" file="count/analyze_diff_expr/results.matrix"/> + <element name="results_matrix_log2_centered" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.centered.dat"/> + <element name="results_matrix_log2_centered_heatmap" delta="100" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/> + <element name="results_matrix_log2" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.dat"/> + <element name="results_matrix_log2_sample_cor" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.sample_cor.dat"/> + <element name="results_matrix_log2_sample_cor_matrix" delta="100" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.sample_cor_matrix.pdf"/> + </output_collection> + <output name="rdata" compare="sim_size" file="count/analyze_diff_expr/results.matrix.RData"/> + </test> + <test> + <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> + <param name="samples" value="count/samples.txt"/> + <param name="DE_results"> + <collection type="list"> + <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results" ftype="tabular" /> + <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" /> + <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" /> + </collection> + </param> + <section name="additional_params"> + <conditional name="GO_enrichment"> + <param name="examine_GO_enrichment" value="yes"/> + <param name="GO_annots" value="count/trinotate/go_annotations.txt"/> + <param name="gene_lengths" value="count/trinotate/genes.lengths.txt"/> + </conditional> + </section> + <assert_command> + <has_text text="--examine_GO_enrichment" /> + <has_text text="--GO_annots" /> + <has_text text="--gene_lengths" /> + </assert_command> + <output_collection name="GOseq_enrichment"> + <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_37-UP.subset.GOseq.enriched" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched"/> + </output_collection> + </test> + </tests> + <help> +<![CDATA[ +Trinity_ assembles transcript sequences from Illumina RNA-Seq data. +This tool extracts the transcripts that are most differentially expressed (most significant FDR and fold-changes), once differential expression analyses have been runned. + +**Inputs** + +This tool uses the raw counts matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool. + +You must describe your samples and replicates with a tabular file looking like this: + +=========== ================ +ConditionA CondA_replicate1 +----------- ---------------- +ConditionA CondA_replicate2 +----------- ---------------- +ConditionB CondB_replicate1 +----------- ---------------- +ConditionB CondB_replicate2 +----------- ---------------- +ConditionC CondC_replicate1 +----------- ---------------- +ConditionC CondC_replicate2 +----------- ---------------- +ConditionC CondC_replicate3 +=========== ================ + +This file can be generated with the 'Describe samples and replicates' tool. +It will probably be the same file as used in the tool 'RNASeq samples quality check for transcript quantification' or in the tool 'Differential expression analysis'. +The names in column 2 must match the names given in the tool 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity'. + +You must also provide as a data collection the files resulting from the differential expression analysis (outputs of tool 'Differential expression analysis'). + +.. _Trinity: http://trinityrnaseq.github.io +]]> + </help> + <expand macro="citation" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,23 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.2.0">trinity</requirement> + <yield/> + </requirements> + </xml> + + <token name="@WRAPPER_VERSION@">2.2.0</token> + + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error in Trinity execution" /> + </stdio> + </xml> + + <xml name="citation"> + <citations> + <citation type="doi">10.1038/nbt.1883</citation> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,7 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR4277|c0_g1_i1 3852.97388871986 161.116814813422 2007.04535176664 -4.57259674791206 0.121601866332754 -37.6030145409076 0 0 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00 +TR4761|c0_g1_i1 1645.20640957447 193.196157329029 919.201283451752 -3.08847487551254 0.143642016580712 -21.5011940728159 1.51733402752078e-102 1.66906743027286e-101 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00 +TR2107|c1_g1_i1 48.9228907410258 7.40521775805688 28.1640542495414 -2.6949883047084 0.431525668867458 -6.24525607429428 4.23106352657394e-10 1.55138995974378e-09 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00 +TR2672|c0_g1_i1 18.3155337236093 2.26581902751323 10.2906763755613 -2.88818323474529 0.724350842979802 -3.98727117216294 6.68376171815065e-05 0.000157545811927837 14.00 29.00 22.00 0.00 4.00 2.00 14.00 4.00 7.00 +TR127|c1_g1_i1 13.461799216177 1.21881296083961 7.34030608850831 -3.33218181130749 0.914685635912973 -3.64298036448506 0.000269499403689035 0.000576210779000196 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 +TR5055|c0_g2_i1 23.3590211688541 5.52768338415684 14.4433522765055 -2.04478780320925 0.562727305023446 -3.63370994255211 0.00027937492315161 0.000576210779000196 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.depleted Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR under_represented_FDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,4 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR131|c0_g1_i1 26.1866396538608 1340.30918254958 683.247911101723 5.67372481552909 0.187406695960058 30.274931140872 2.45144211418965e-201 4.04487948841292e-200 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00 +TR3091|c0_g1_i1 16.7444693227929 328.569936894811 172.657203108802 4.29039998257063 0.240421038467916 17.8453599980735 3.14072644239509e-71 2.59109931497595e-70 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00 +TR3788|c0_g1_i1 19.5075441237117 134.95369713876 77.2306206312357 2.77038513264018 0.262760026053246 10.5434040871909 5.44900939296595e-26 2.56881871382681e-25 17.00 30.00 22.00 91.00 132.00 125.00 32.00 22.00 27.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset.GOseq.depleted Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR under_represented_FDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset.GOseq.enriched Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,7 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR4277|c0_g1_i1 4705.34614971641 162.902721493704 2434.12443560506 -4.84860951090545 0.124597307945428 -38.9142397284305 0 0 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00 +TR4761|c0_g1_i1 2012.6141923276 384.620292965437 1198.61724264652 -2.38450946693381 0.143863830576436 -16.5747669680385 1.06073316501088e-61 1.34359534234711e-60 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00 +TR2107|c1_g1_i1 59.5986596731862 1.89840873462066 30.7485342039034 -4.81058600791914 0.641850436461167 -7.49487066557473 6.63637683134955e-14 2.29256654173894e-13 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00 +TR127|c1_g1_i1 16.3791628279609 1.58772512712498 8.98344397754296 -3.19771077466237 0.834376974262452 -3.83245328346816 0.00012687169720824 0.000267840249661839 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 +TR1894|c2_g1_i1 16.2826445742552 1.67571344127509 8.97917900776516 -3.15659686337855 0.834779400611257 -3.7813545244015 0.00015597736029041 0.000307529893573321 21.00 14.00 11.00 1.00 2.00 5.00 1.00 3.00 1.00 +TR5055|c0_g2_i1 28.6665933385886 6.05959103586122 17.3630921872249 -2.17768048931004 0.577307428800381 -3.77213314894485 0.000161857838722801 0.000307529893573321 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.depleted Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR under_represented_FDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,2 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR go_term +GO:0008270 0.0469428206943769 0.996332779511344 3 6 zinc ion binding MF 0.790651800018629 MF zinc ion binding
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,5 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR131|c0_g1_i1 32.0461070493257 1436.30905989883 734.177583474076 5.48367743370229 0.196017912869615 27.9753893581648 3.23827538807456e-172 6.15272323734167e-171 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00 +TR3091|c0_g1_i1 20.4914097091341 321.651020117047 171.071214913091 3.96886910507283 0.256323110469072 15.4838519937191 4.45952081812589e-54 4.2365447772196e-53 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00 +TR2779|c0_g1_i1 191.51955185349 1058.15934185376 624.839446853626 2.46616535412611 0.177102083131526 13.9251064161374 4.4587691300744e-44 3.38866453885655e-43 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00 +TR5075|c0_g1_i1 19.3833722195684 136.98672801182 78.1850501156942 2.80049241151413 0.293976352213923 9.52625063350759 1.63066468983638e-21 8.85217974482605e-21 13.00 22.00 21.00 6.00 8.00 10.00 163.00 121.00 142.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.depleted Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR under_represented_FDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.enriched Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,1 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,3 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR2779|c0_g1_i1 195.849684476753 966.924129135581 581.386906806167 2.25621220756415 0.156114979193812 14.4522467940961 2.42639762934434e-47 5.82335431042642e-46 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00 +TR24|c0_g1_i1 39.3724575919554 183.288101009647 111.330279300801 2.11680322693425 0.240338854880295 8.80757806717753 1.27878744153922e-18 7.67272464923531e-18 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.depleted Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR under_represented_FDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.enriched Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/results.matrix Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,14 @@ + wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR24|c0_g1_i1 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00 +TR4277|c0_g1_i1 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00 +TR2779|c0_g1_i1 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00 +TR2672|c0_g1_i1 14.00 29.00 22.00 0.00 4.00 2.00 14.00 4.00 7.00 +TR127|c1_g1_i1 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 +TR2107|c1_g1_i1 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00 +TR5055|c0_g2_i1 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00 +TR3091|c0_g1_i1 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00 +TR4761|c0_g1_i1 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00 +TR131|c0_g1_i1 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00 +TR5075|c0_g1_i1 13.00 22.00 21.00 6.00 8.00 10.00 163.00 121.00 142.00 +TR1894|c2_g1_i1 21.00 14.00 11.00 1.00 2.00 5.00 1.00 3.00 1.00 +TR3788|c0_g1_i1 17.00 30.00 22.00 91.00 132.00 125.00 32.00 22.00 27.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/results.matrix.log2.centered.dat Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,14 @@ +wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR24|c0_g1_i1 0.106533882165825 -0.313797916782532 0.025003996669227 -1.19180739240392 -1.23133575659056 -1.2719777410879 1.39963914188743 1.22079106142351 1.25695072471892 +TR4277|c0_g1_i1 3.24415794782388 3.31812623217364 3.18414689752048 -1.98611482817144 -1.80411699442855 -1.51461037723356 -1.44630436384266 -1.5322044372483 -1.46308007659348 +TR2779|c0_g1_i1 -0.795433018475884 -1.23380302158535 -0.574143153586594 -1.13287411273457 -0.795433018475884 -0.712970858283911 1.74646076035339 1.75438767612502 1.74380874666379 +TR2672|c0_g1_i1 0.965440325233136 1.96544032523314 1.58211168568163 -2.94145027037538 -0.619522175488021 -1.35648776965423 0.965440325233136 -0.619522175488021 0.0585497296246169 +TR127|c1_g1_i1 1.25755965737847 2.52059406321227 2.02309440374145 -0.479405936787734 -2.06436843750889 -1.06436843750889 -0.0643684375088904 -1.06436843750889 -1.06436843750889 +TR2107|c1_g1_i1 2.49178842221691 2.62929194596684 2.16986032732955 -0.607747251334006 -0.607747251334006 -0.41510217339161 -1.41510217339161 -2.41510217339161 -1.83013967267045 +TR5055|c0_g2_i1 1.90528891290538 0.865760548718745 1.50319046933404 -0.982236357836205 -0.304164452723568 -1.30416445272357 -0.982236357836205 -0.982236357836205 0.280798047997588 +TR3091|c0_g1_i1 -2.42438780178849 -2.77802475640319 -2.62602166295814 1.02359379610527 1.32351327005887 1.20686835120661 1.43575453462855 1.4783149968566 1.36038927229391 +TR4761|c0_g1_i1 2.06406810079911 1.80544476674762 1.90822498634624 -1.67981690730689 -1.51400801433681 -1.59017969482221 -0.339510283104669 -0.357888812419525 -0.296334141902888 +TR131|c0_g1_i1 -3.50802026981862 -3.6944333940495 -3.55241438917708 1.41625240401813 1.71671228997234 1.68718414007205 1.98577454287534 1.99158406095747 1.95736061514986 +TR5075|c0_g1_i1 -1.04544737992556 -0.329240345926152 -0.393370683345868 -2.04544737992556 -1.68287730054085 -1.39337068334587 2.50474970263492 2.07793503557972 2.30706903479522 +TR1894|c2_g1_i1 2.11263053903627 1.56008951600749 1.23816142112012 -1.34680107960103 -0.761838578879876 0.238161421120124 -1.34680107960103 -0.346801079601032 -1.34680107960103 +TR3788|c0_g1_i1 -1.22775484082629 -0.443483531881724 -0.874117886211586 1.12588211378841 1.65760259323259 1.57960008123132 -0.353285722910146 -0.874117886211586 -0.590324920210995
Binary file test-data/count/analyze_diff_expr/results.matrix.log2.centered.genes_vs_samples_heatmap.pdf has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/results.matrix.log2.dat Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,14 @@ +wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR24|c0_g1_i1 6.5077946401987 6.08746284125034 6.4262647547021 5.20945336562895 5.16992500144231 5.12928301694497 7.8008998999203 7.62205181945638 7.65821148275179 +TR4277|c0_g1_i1 12.1250905393033 12.199058823653 12.0650794889999 6.89481776330794 7.07681559705083 7.36632221424582 7.43462822763672 7.34872815423108 7.4178525148859 +TR2779|c0_g1_i1 7.54689445988764 7.10852445677817 7.76818432477693 7.20945336562895 7.54689445988764 7.62935662007961 10.0887882387169 10.0967151544885 10.0861362250273 +TR2672|c0_g1_i1 3.90689059560852 4.90689059560852 4.52356195605701 0 2.32192809488736 1.58496250072116 3.90689059560852 2.32192809488736 3 +TR127|c1_g1_i1 3.32192809488736 4.58496250072116 4.08746284125034 1.58496250072116 0 1 2 1 1 +TR2107|c1_g1_i1 5.90689059560852 6.04439411935845 5.58496250072116 2.8073549220576 2.8073549220576 3 2 1 1.58496250072116 +TR5055|c0_g2_i1 5.20945336562895 4.16992500144231 4.8073549220576 2.32192809488736 3 2 2.32192809488736 2.32192809488736 3.58496250072116 +TR3091|c0_g1_i1 4.52356195605701 4.16992500144231 4.32192809488736 7.97154355395077 8.27146302790437 8.1548181090521 8.38370429247405 8.4262647547021 8.30833903013941 +TR4761|c0_g1_i1 11.0292872269682 10.7706638929168 10.8734441125154 7.28540221886225 7.45121111183233 7.37503943134692 8.62570884306447 8.60733031374961 8.66888498426625 +TR131|c0_g1_i1 5.04439411935845 4.85798099512757 5 9.96866679319521 10.2691266791494 10.2395985292491 10.5381889320524 10.5439984501345 10.5097750043269 +TR5075|c0_g1_i1 3.8073549220576 4.52356195605701 4.4594316186373 2.8073549220576 3.16992500144231 3.4594316186373 7.35755200461808 6.93073733756289 7.15987133677839 +TR1894|c2_g1_i1 4.4594316186373 3.90689059560852 3.58496250072116 1 1.58496250072116 2.58496250072116 1 2 1 +TR3788|c0_g1_i1 4.16992500144231 4.95419631038687 4.52356195605701 6.52356195605701 7.05528243550119 6.97727992349992 5.04439411935845 4.52356195605701 4.8073549220576
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor.dat Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,10 @@ +wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +wt_37_2 1 0.968650822800566 0.985499030254524 0.457364683078012 0.443497697874748 0.451451348748615 0.41961787977306 0.444203836374748 0.448348619980356 +wt_37_3 0.968650822800566 1 0.98879028662025 0.400031307625771 0.378330685571456 0.396636302989378 0.39057945325073 0.383299487197462 0.388022080096891 +wt_37_1 0.985499030254524 0.98879028662025 1 0.452638132682111 0.434834315692609 0.44176483058741 0.461437515072935 0.462172448553839 0.473652431554024 +wt_GSNO_3 0.457364683078012 0.400031307625771 0.452638132682111 1 0.965144031362199 0.979742518682039 0.844139129634192 0.862862111399854 0.857171072391268 +wt_GSNO_1 0.443497697874748 0.378330685571456 0.434834315692609 0.965144031362199 1 0.983818328020852 0.858668155107621 0.871693931267863 0.876908826664397 +wt_GSNO_2 0.451451348748615 0.396636302989378 0.44176483058741 0.979742518682039 0.983818328020852 1 0.854388461031158 0.878292745544781 0.861156659158544 +wt_ph8_3 0.41961787977306 0.39057945325073 0.461437515072935 0.844139129634192 0.858668155107621 0.854388461031158 1 0.984071267766826 0.98764423106737 +wt_ph8_1 0.444203836374748 0.383299487197462 0.462172448553839 0.862862111399854 0.871693931267863 0.878292745544781 0.984071267766826 1 0.989191009161984 +wt_ph8_2 0.448348619980356 0.388022080096891 0.473652431554024 0.857171072391268 0.876908826664397 0.861156659158544 0.98764423106737 0.989191009161984 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,39 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj +TR4277|c0_g1_i1 3852.97388871986 161.116814813422 2007.04535176664 -4.57259674791206 0.121601866332754 -37.6030145409076 0 0 +TR131|c0_g1_i1 26.1866396538608 1340.30918254958 683.247911101723 5.67372481552909 0.187406695960058 30.274931140872 2.45144211418965e-201 4.04487948841292e-200 +TR4761|c0_g1_i1 1645.20640957447 193.196157329029 919.201283451752 -3.08847487551254 0.143642016580712 -21.5011940728159 1.51733402752078e-102 1.66906743027286e-101 +TR3091|c0_g1_i1 16.7444693227929 328.569936894811 172.657203108802 4.29039998257063 0.240421038467916 17.8453599980735 3.14072644239509e-71 2.59109931497595e-70 +TR3638|c0_g1_i1 583.00358519031 183.754416330029 383.37900076017 -1.66018915730897 0.144484444213305 -11.4904352945982 1.47367477630653e-30 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0.354180332604713 +TR2278|c0_g1_i1 486.5272515724 448.140178813055 467.333715192727 -0.118822731208233 0.119975347874694 -0.990392887481645 0.321982120549739 0.354180332604713 +TR2011|c5_g1_i1 5.60408627995835 7.88255079488408 6.74331853742122 0.488779860259128 0.689341019893534 0.70905378637502 0.478291099766969 0.509148590074515 +TR2182|c3_g2_i6 2.24974854180929 1.3031439398571 1.77644624083319 -0.780861388045469 1.28191780274725 -0.609135302101293 0.54243475986365 0.559385846109389 +TR3249|c0_g1_i1 1.12573841927462 2.128954842887 1.62734663108081 0.761533075632955 1.28978972955114 0.590431958159547 0.554901090261946 1 +TR1678|c0_g1_i1 0.595141051681226 0.700100668536423 0.647620860108824 0.247986780508542 1.73527723872539 0.142909026277954 0.886362029808798 1 +TR1122|c0_g1_i1 1.41370386226057 1.3031439398571 1.35842390105883 -0.16283641618004 1.43170451886811 -0.113736049606644 0.909447034479058 1 +TR1982|c2_g1_i1 5.73684100209948 5.71221669652109 5.72452884931028 0.0102126833240523 0.713573951255734 0.0143120181252136 0.988581051536513 0.988581051536513 +TR2090|c0_g1_i1 0 9.55638889228537 4.77819444614269 3.06235120305875 2.04796345977052 1.49531535264887 NA 1
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,39 @@ +logFC logCPM PValue FDR +TR131|c0_g1_i1 5.8364197685119 16.0402624962907 0 0 +TR4277|c0_g1_i1 -4.41329137350676 17.4523259866001 0 0 +TR3091|c0_g1_i1 4.45193883524837 14.0450613692144 2.75977672027703e-191 3.0023764016608e-190 +TR4761|c0_g1_i1 -2.92753980838104 16.3343761538543 3.16039621227453e-191 3.0023764016608e-190 +TR2487|c0_g1_i1 1.58705373680526 15.8895982491351 1.69098562804069e-123 1.28514907731092e-122 +TR1479|c0_g1_i1 1.67068054401246 14.5625418524933 4.82942248775202e-81 3.05863424224295e-80 +TR3638|c0_g1_i1 -1.49936398500381 15.1049693447894 1.31792237756209e-64 7.15443576390849e-64 +TR3854|c0_g1_i1 0.756865722480515 17.5147652035186 8.35417282711821e-40 3.96823209288115e-39 +TR2122|c0_g2_i2 0.903942128151819 13.8996874045924 3.62505920095794e-13 1.53058055151558e-12 +TR2844|c0_g1_i1 0.707836713891037 14.1854217777842 1.87464339893047e-12 7.1236449159358e-12 +TR3788|c0_g1_i1 2.92403132462783 12.8779140660683 1.50355808369265e-09 5.19410974366551e-09 +TR4669|c0_g2_i1 10.5374101870061 13.0322839834498 3.83881845042015e-08 1.21562584263305e-07 +TR2672|c0_g1_i1 -2.77697626464917 10.2324144831548 6.6653206315345e-08 1.9483244922947e-07 +TR4163|c0_g1_i1 -0.420124679057253 14.7293558096347 2.6407759845512e-06 7.16782052949613e-06 +TR2107|c1_g1_i1 -2.54740509831049 11.4796217709789 1.31520100526586e-05 3.33184254667352e-05 +TR2779|c0_g1_i1 0.57151150266807 14.0680960027645 7.44562831370785e-05 0.000176833672450561 +TR127|c1_g1_i1 -3.25307512484374 9.84850588284066 0.000331345441643876 0.000740654516615722 +TR1894|c2_g1_i1 -1.90241917506329 9.93135664117576 0.00432077639530722 0.00912163905675968 +TR5055|c0_g2_i1 -1.8950478385132 10.598211984773 0.00591755208579545 0.0118351041715909 +TR2090|c0_g1_i1 6.41050251489574 9.11635750687386 0.0113096900461153 0.021488411087619 +TR5212|c0_g1_i1 0.867439938079617 13.0331405503531 0.0317111501604761 0.0573820812427663 +TR3807|c0_g1_i1 -2.67963301995355 8.56046890206839 0.0557212159288941 0.0962457366044534 +TR1449|c0_g1_i1 -0.636836241811875 13.7146214195087 0.0845994280568489 0.139772968093924 +TR4084|c0_g1_i1 0.527023803952886 13.333880353991 0.19596368831627 0.301997237380275 +TR1891|c0_g1_i1 0.481345196849859 13.5019985083809 0.198682393013339 0.301997237380275 +TR24|c0_g1_i1 -0.590671163985234 12.3854267629296 0.21115333494008 0.308608720297039 +TR1837|c2_g1_i1 2.67943439258847 8.19914223144978 0.242162966500684 0.336820885113627 +TR4859|c0_g1_i1 -1.04273446956489 9.43870802835889 0.248183810083725 0.336820885113627 +TR939|c0_g1_i1 0.361607908864682 13.0838256643577 0.341542524228359 0.447538480023367 +TR2011|c5_g1_i1 0.672074276530526 9.63297397547156 0.357699118838244 0.453085550528442 +TR5075|c0_g1_i1 -0.617596452044795 10.4317228965746 0.378826401739151 0.464367847293153 +TR3249|c0_g1_i1 0.936067544593607 8.34110243846743 0.532174466327564 0.631957178763983 +TR1492|c0_g1_i2 -0.0311770185465736 17.1360846492483 0.562063331952301 0.647224442854165 +TR2278|c0_g1_i1 0.0373157391528861 15.4251088322423 0.63557189922311 0.710345063837593 +TR2182|c3_g2_i6 -0.665499179094881 8.45651702709919 0.835363486459349 0.906966071013008 +TR1982|c2_g1_i1 0.176241441184615 9.49445846907393 0.904611213246767 0.954867391760477 +TR1678|c0_g1_i1 0.476522568809639 7.93710096737952 1 1 +TR1122|c0_g1_i1 -0.015204817268041 8.26206767263358 1 1
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,39 @@ +logFC logCPM PValue FDR +TR131|c0_g1_i1 5.8235943392439 16.1127963113785 7.14846919291531e-10 2.71641829330782e-08 +TR4277|c0_g1_i1 -4.41182125975734 17.3835558041266 1.56187740933885e-09 2.96756707774382e-08 +TR3091|c0_g1_i1 4.43711915085412 14.1189484156579 4.80332538807657e-08 5.96619459206176e-07 +TR2487|c0_g1_i1 1.58597331690052 15.926957585609 6.28020483374923e-08 5.96619459206176e-07 +TR4761|c0_g1_i1 -2.92047098366841 16.2714320125634 5.50582910815067e-07 4.18443012219451e-06 +TR1479|c0_g1_i1 1.67737907773679 14.6004783880878 9.51214752241748e-07 5.52604916020242e-06 +TR3638|c0_g1_i1 -1.50273266496817 15.0596817330556 1.02518921423282e-06 5.52604916020242e-06 +TR3788|c0_g1_i1 2.93902285611693 12.9382150715361 2.41689084349911e-06 1.02046502281074e-05 +TR3854|c0_g1_i1 0.759398996973938 17.5343629610585 1.16337877056893e-06 5.52604916020242e-06 +TR2107|c1_g1_i1 -2.46238704341773 11.2600018185657 0.000160625103091043 0.000554886719769058 +TR2122|c0_g2_i2 0.898555189960494 13.9141616710754 0.000116065228333624 0.000441047867667773 +TR2844|c0_g1_i1 0.712285451514242 14.1964395706942 0.000226456956836179 0.0007171136966479 +TR5212|c0_g1_i1 0.877383155201317 13.0382243238454 0.00044264831250554 0.00129389506732389 +TR4163|c0_g1_i1 -0.417753044994067 14.7100536369854 0.00073550773195026 0.00199637812957928 +TR1449|c0_g1_i1 -0.639430683731338 13.6750299459863 0.0021688744394372 0.00549448191324091 +TR2672|c0_g1_i1 -2.89090970573392 9.81450205355949 0.0110308904582196 0.0220617809164392 +TR127|c1_g1_i1 -3.10441694967501 9.33201892428652 0.0147505107490706 0.0271381068158418 +TR939|c0_g1_i1 0.363392391144623 13.0700139113805 0.00528218330196852 0.0125451853421752 +TR5055|c0_g2_i1 -1.80082179647401 10.290740057161 0.014997374819281 0.0271381068158418 +TR1894|c2_g1_i1 -1.81920882927282 9.4761161835092 0.0211021355265418 0.0348643978264604 +TR1891|c0_g1_i1 0.477106166889499 13.4994625375761 0.00640932243854848 0.0143267207449907 +TR1837|c2_g1_i1 2.21852868850051 7.02301103616459 0.041457300582048 0.063015096884713 +TR3807|c0_g1_i1 -1.9168529396959 7.35599058475032 0.0566225608328877 0.0827560504480666 +TR2779|c0_g1_i1 0.600059279980753 14.0739938889057 0.00964636468216327 0.0203645476623447 +TR24|c0_g1_i1 -0.588697529952342 12.3096839182028 0.0194904179372949 0.0336652673462366 +TR4859|c0_g1_i1 -1.06821251099455 8.91301871295058 0.111617387620425 0.157091138132451 +TR2090|c0_g1_i1 2.22339391910091 8.98366602727699 0.254495907488744 0.322361482819076 +TR4084|c0_g1_i1 0.567566096899832 13.3297126444574 0.036433281659912 0.0576860292948607 +TR2182|c3_g2_i6 -1.0316496616205 7.37334712818428 0.34572838664377 0.423796086853654 +TR2011|c5_g1_i1 0.791574287810665 9.32879226678442 0.161547389819689 0.211682786660282 +TR5075|c0_g1_i1 -0.550289601556128 10.1785868671389 0.12853444928267 0.174439609740767 +TR1678|c0_g1_i1 0.331221243897688 5.95523974949609 0.7547763751788 0.806418050624271 +TR4669|c0_g2_i1 6.27373933776222 13.1239272719772 0.48073138273468 0.553569471027814 +TR1122|c0_g1_i1 -0.199192308627843 7.01379133029712 0.87736931102229 0.87736931102229 +TR3249|c0_g1_i1 0.258869539778469 7.31927198802943 0.798677928444158 0.820263818402108 +TR1982|c2_g1_i1 0.132112224684827 9.08491674138301 0.763974995328257 0.806418050624271 +TR2278|c0_g1_i1 0.0407550618622219 15.423513715505 0.613273487399665 0.685423309446684 +TR1492|c0_g1_i2 -0.0324123498367541 17.1356104672946 0.389074079094509 0.462025468924729
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,39 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj +TR4277|c0_g1_i1 4705.34614971641 162.902721493704 2434.12443560506 -4.84860951090545 0.124597307945428 -38.9142397284305 0 0 +TR131|c0_g1_i1 32.0461070493257 1436.30905989883 734.177583474076 5.48367743370229 0.196017912869615 27.9753893581648 3.23827538807456e-172 6.15272323734167e-171 +TR4761|c0_g1_i1 2012.6141923276 384.620292965437 1198.61724264652 -2.38450946693381 0.143863830576436 -16.5747669680385 1.06073316501088e-61 1.34359534234711e-60 +TR3091|c0_g1_i1 20.4914097091341 321.651020117047 171.071214913091 3.96886910507283 0.256323110469072 15.4838519937191 4.45952081812589e-54 4.2365447772196e-53 +TR2779|c0_g1_i1 191.51955185349 1058.15934185376 624.839446853626 2.46616535412611 0.177102083131526 13.9251064161374 4.4587691300744e-44 3.38866453885655e-43 +TR1492|c0_g1_i2 2006.11782336441 890.823502721036 1448.47066304272 -1.17029110983798 0.12207086547883 -9.58698134274255 9.06997941755552e-22 5.74432029778516e-21 +TR5075|c0_g1_i1 19.3833722195684 136.98672801182 78.1850501156942 2.80049241151413 0.293976352213923 9.52625063350759 1.63066468983638e-21 8.85217974482605e-21 +TR1891|c0_g1_i1 131.416087212132 376.595292171713 254.005689691923 1.51493508389526 0.17090866237033 8.86400409952692 7.71909159725621e-19 3.6665685086967e-18 +TR2487|c0_g1_i1 418.818667162757 965.862817209246 692.340742186001 1.20547893236143 0.136832960243688 8.80985787499278 1.25304626500959e-18 5.29063978559604e-18 +TR3638|c0_g1_i1 713.131183384274 326.063958913919 519.597571149096 -1.1281436752687 0.141731779309567 -7.95970868893582 1.72444792020844e-15 6.55290209679206e-15 +TR2107|c1_g1_i1 59.5986596731862 1.89840873462066 30.7485342039034 -4.81058600791914 0.641850436461167 -7.49487066557473 6.63637683134955e-14 2.29256654173894e-13 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-2.61274053843141 0.973661400721484 -2.68341801009608 0.00728738414676855 0.0115383582323835 +TR2672|c0_g1_i1 22.3129914439134 7.89947501226409 15.1062332280887 -1.45907440559266 0.562189545530202 -2.59534247335852 0.0094496708578661 0.0143634997039565 +TR3807|c0_g1_i1 4.23896204531587 0.352255997713617 2.29560902151474 -3.05008419968594 1.43726100452922 -2.12215052803511 0.0338250994349076 0.0494366837894803 +TR3249|c0_g1_i1 1.36481976577862 4.37661229401476 2.87071602989669 1.51948727816201 1.15409756308282 1.31660210260141 0.187972033660362 0.255148785128113 +TR1859|c3_g1_i1 0.361569353912422 2.25550826604853 1.30853880998047 2.09887277242766 1.59427549709957 1.31650569568817 0.188004367989136 0.255148785128113 +TR1982|c2_g1_i1 7.00144976454503 11.520013112092 9.26073143831853 0.70490953188932 0.647715898283926 1.0883004937148 0.276462472665158 0.362261171078483 +TR3854|c0_g1_i1 1925.26464813324 2107.16376011081 2016.21420412203 0.130534071096341 0.124633726123269 1.04734147936199 0.29494211171073 0.373593341500258 +TR5212|c0_g1_i1 80.2050001877881 94.8352723753388 87.5201362815635 0.236773654582184 0.240888724170321 0.982917134862537 0.325648223857982 0.399181693761397 +TR1837|c2_g1_i1 0.377330628439655 1.67813520813222 1.02773291828594 1.63744709452968 1.70484764845029 0.960465350682869 0.336821061516539 0.39997501055089 +TR2844|c0_g1_i1 193.030766468894 213.82243412349 203.426600296192 0.144163413939115 0.182129405153131 0.791543868591151 0.428626687374099 0.493570124855023 +TR1122|c0_g1_i1 1.69354093201913 0.660517838352177 1.17702938518565 -1.10951489814723 1.57444243758247 -0.704703374135971 0.48099485111646 0.537582480659573 +TR2011|c5_g1_i1 6.84875389533898 4.81927837273561 5.8340161340373 -0.467994718304978 0.83497566164615 -0.560489053516039 0.575145904101733 0.62444412445331 +TR2182|c3_g2_i6 2.76248771922916 1.94482465855284 2.353656188891 -0.463555959442342 1.17585679724627 -0.394228243207794 0.69341253558072 0.731935454224094 +TR3788|c0_g1_i1 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Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,39 @@ +logFC logCPM PValue FDR +TR131|c0_g1_i1 5.83867709149149 16.0447742820606 3.67956255674e-64 1.3982337715612e-62 +TR3091|c0_g1_i1 4.35104356420213 13.9337836495047 7.47918124727105e-59 1.4210444369815e-57 +TR4277|c0_g1_i1 -4.51249642920563 17.4585638169146 1.30305812944242e-53 1.65054029729373e-52 +TR5075|c0_g1_i1 3.18286810352713 12.8084040893566 8.25600206225396e-24 7.84320195914126e-23 +TR2107|c1_g1_i1 -4.48477961203985 11.2510359028096 1.80754966502889e-22 1.37373774542196e-21 +TR2779|c0_g1_i1 2.75442228103487 15.7797198210508 8.23352696880425e-15 5.21456708024269e-14 +TR1891|c0_g1_i1 1.85607282303223 14.4424161372431 4.82341414399837e-12 2.61842482102769e-11 +TR4761|c0_g1_i1 -2.05815692521639 16.4916266891202 6.53530817860542e-12 3.10427138483757e-11 +TR1479|c0_g1_i1 1.43256512308186 14.3771181295432 1.13197856555697e-09 4.77946505457389e-09 +TR2122|c0_g2_i2 1.63807722824331 14.4300672231344 2.54380104198531e-09 9.66644395954419e-09 +TR24|c0_g1_i1 1.56169455062581 13.613754007054 1.01137959952142e-08 3.49385679834671e-08 +TR2487|c0_g1_i1 1.52157644373511 15.8810635663776 2.37540305111961e-07 7.52210966187877e-07 +TR4084|c0_g1_i1 0.991060679215133 13.5661427311877 4.21767858359174e-07 1.23285989366528e-06 +TR1678|c0_g1_i1 3.62458577193226 9.02581543875671 1.43837087677047e-05 3.90414952266271e-05 +TR127|c1_g1_i1 -2.90111481011278 9.73961125813442 2.21824302925283e-05 5.61954900744051e-05 +TR1894|c2_g1_i1 -2.85359093751189 9.70265145133598 3.82707393478771e-05 9.08930059512081e-05 +TR5055|c0_g2_i1 -1.8545312748531 10.5508309427169 0.000561739096452478 0.0012556520979526 +TR2090|c0_g1_i1 5.85461418677349 8.72713197001274 0.000625444406369261 0.00132038263566844 +TR4859|c0_g1_i1 -2.31469487039419 9.12085022188999 0.00236706272759891 0.00473412545519782 +TR1492|c0_g1_i2 -0.847097868783511 16.8160271449712 0.00265383515294934 0.00504228679060374 +TR3638|c0_g1_i1 -0.812580107843708 15.3469752226999 0.00403607816905259 0.00730337954399992 +TR3807|c0_g1_i1 -2.92018331334326 8.37863764275674 0.0119536481076316 0.0206472103677272 +TR1449|c0_g1_i1 -0.576747771663695 13.7363876885022 0.0130185393324759 0.0215088910710471 +TR1982|c2_g1_i1 1.11743546508384 9.86122459596308 0.024471659211255 0.0382656346855499 +TR2672|c0_g1_i1 -1.09825528852042 10.4080374441724 0.025174759661546 0.0382656346855499 +TR3249|c0_g1_i1 2.00776956676821 8.66772655901099 0.0275363688345113 0.0402454621427472 +TR5212|c0_g1_i1 0.582012857882519 12.8600915149255 0.0318599127004672 0.0448398771339909 +TR4163|c0_g1_i1 -0.585935901552979 14.6858409740027 0.0333717283041774 0.0452902026985264 +TR2844|c0_g1_i1 0.484938504762758 14.0537413817093 0.0410237194953782 0.0537552186491163 +TR1859|c3_g1_i1 2.64648031785777 8.0811923384908 0.0677782555815868 0.0858524570700099 +TR2278|c0_g1_i1 -0.462893051132405 15.2205527935145 0.0990317248813937 0.121393727273966 +TR3854|c0_g1_i1 0.45233145936844 17.3656486469949 0.115995274036176 0.13774438791796 +TR3788|c0_g1_i1 0.512277745155381 11.1125640718165 0.129462204245195 0.149077689736891 +TR939|c0_g1_i1 0.343195417039388 13.0829763503018 0.196684960972624 0.219824368145874 +TR1837|c2_g1_i1 2.21076601464763 7.9226544260522 0.248563909756302 0.269869387735413 +TR1122|c0_g1_i1 -0.860567840252952 7.98418712954456 0.72405804618472 0.764283493194982 +TR2011|c5_g1_i1 -0.075980865610854 9.27931055760989 0.901508002533997 0.925873083683564 +TR2182|c3_g2_i6 -0.147124070779728 8.45393312498213 1 1
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,39 @@ +logFC logCPM PValue FDR +TR131|c0_g1_i1 5.89108692370307 16.0946870940125 4.52958285205525e-36 1.721241483781e-34 +TR4277|c0_g1_i1 -4.47812345668175 17.3786096664403 1.7008141018303e-32 3.23154679347758e-31 +TR3091|c0_g1_i1 4.37454375877296 13.9751350003907 7.58044859691792e-23 9.60190155609603e-22 +TR2779|c0_g1_i1 2.89398117484377 15.8061264352363 3.97828335136821e-18 3.7793691837998e-17 +TR5075|c0_g1_i1 3.21512246000432 12.8334153580766 2.0588784190888e-14 1.56474759850749e-13 +TR2107|c1_g1_i1 -4.32040270723487 11.0762608486921 9.69490500265428e-11 6.14010650168104e-10 +TR4761|c0_g1_i1 -2.00464775189483 16.4172477083723 2.27235196662378e-10 1.23356249616719e-09 +TR1891|c0_g1_i1 1.89490003648365 14.4620196202787 1.18363400337593e-09 5.62226151603565e-09 +TR2122|c0_g2_i2 1.68823123696301 14.4430864744705 3.40183177422869e-08 1.436328971341e-07 +TR24|c0_g1_i1 1.665273448047 13.6146325155501 1.25297628243395e-07 4.76130987324901e-07 +TR2487|c0_g1_i1 1.57111929409713 15.8914511338271 3.01913153313087e-07 1.04297271144521e-06 +TR1479|c0_g1_i1 1.45195340320994 14.3929474544484 1.34694977997748e-06 4.2653409699287e-06 +TR1678|c0_g1_i1 3.32711159096413 8.62991286220581 4.44668660347576e-05 0.000129980069947753 +TR127|c1_g1_i1 -2.68488776770857 9.36026180000128 0.000136507461427459 0.00037052025244596 +TR1894|c2_g1_i1 -2.65840371977461 9.30640094015976 0.000158988679158599 0.000402771320535117 +TR2090|c0_g1_i1 3.12073361486577 8.21515298661506 0.000414922023762837 0.000985439806436737 +TR5055|c0_g2_i1 -1.75449782198233 10.3047459168783 0.000987360143376457 0.0020844269693503 +TR4084|c0_g1_i1 0.990738086664283 13.5812840323914 0.000929878324478984 0.00207855154883538 +TR4859|c0_g1_i1 -2.03844841522755 8.5557148387818 0.00574511253124233 0.0114902250624847 +TR3807|c0_g1_i1 -2.27805436961797 7.32408068149202 0.00831980659467625 0.0150548881236999 +TR1859|c3_g1_i1 2.08358066039446 6.92308482511994 0.0216139227266133 0.0357099592874481 +TR1492|c0_g1_i2 -0.80292474159496 16.7717103141256 0.00797659176853916 0.0150548881236999 +TR3638|c0_g1_i1 -0.765536214533451 15.2959378061905 0.00929698340782949 0.0160584258862509 +TR2672|c0_g1_i1 -1.15555384827173 10.1973122527932 0.0235572978271919 0.0372990548930539 +TR3249|c0_g1_i1 1.48866796495104 8.06119288435276 0.0588654345124954 0.0794847966327657 +TR1982|c2_g1_i1 1.06368641289493 9.64628067316551 0.0510418091524593 0.0745995672228252 +TR1837|c2_g1_i1 1.43890969571076 6.48444225997254 0.130037630852572 0.154419686637429 +TR5212|c0_g1_i1 0.63168831011067 12.8380836623566 0.0456316928604782 0.0693601731479268 +TR4163|c0_g1_i1 -0.545743678134199 14.6411189904126 0.0582697662607788 0.0794847966327657 +TR1449|c0_g1_i1 -0.549932747054717 13.6939664483469 0.0606594500618475 0.0794847966327657 +TR2844|c0_g1_i1 0.508967050135572 14.0451022220879 0.0750763100520493 0.0950966593992624 +TR3854|c0_g1_i1 0.504473372285636 17.3527799714624 0.0956174473541405 0.117208483853463 +TR1122|c0_g1_i1 -0.501746583160273 6.50836597017328 0.595453777887275 0.628534543325457 +TR3788|c0_g1_i1 0.524753873079964 11.0311382344715 0.215975804877357 0.234488016723988 +TR2278|c0_g1_i1 -0.424377145183038 15.1829447141358 0.145500439954072 0.167545961159234 +TR2182|c3_g2_i6 0.0429471548350905 7.57134083040984 0.956400717774849 0.956400717774849 +TR939|c0_g1_i1 0.398499350568058 13.0523653134109 0.192129988432482 0.214733516483362 +TR2011|c5_g1_i1 0.0410416962762211 8.85697121679121 0.9477445647389 0.956400717774849
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,40 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj +TR2779|c0_g1_i1 195.849684476753 966.924129135581 581.386906806167 2.25621220756415 0.156114979193812 14.4522467940961 2.42639762934434e-47 5.82335431042642e-46 +TR1891|c0_g1_i1 128.246229498835 343.028289972482 235.637259735659 1.40479466067472 0.104376051709838 13.4589749052781 2.72672776456232e-41 3.27207331747478e-40 +TR4761|c0_g1_i1 184.029205648389 351.782300021135 267.905752834762 0.934185686537064 0.0945413616088594 9.88123791152932 5.0208774429335e-23 4.0167019543468e-22 +TR24|c0_g1_i1 39.3724575919554 183.288101009647 111.330279300801 2.11680322693425 0.240338854880295 8.80757806717753 1.27878744153922e-18 7.67272464923531e-18 +TR3638|c0_g1_i1 174.266398355818 297.555274221606 235.910836288712 0.75598517202537 0.0975355931355663 7.75086455848598 9.12689947000201e-15 3.81892706573808e-14 +TR2122|c0_g2_i2 190.673533226329 328.707071692642 259.690302459485 0.782528370953275 0.101034702024136 7.74514454218254 9.54731766434521e-15 3.81892706573808e-14 +TR2278|c0_g1_i1 426.804298570637 315.99710709695 371.400702833793 -0.429046906426044 0.106511998284025 -4.02815563822158 5.62161256784655e-05 0.000192741002326167 +TR4084|c0_g1_i1 115.544575735664 157.970364768418 136.757470252041 0.435378746345168 0.157905703989027 2.75720721510747 0.00582973950434901 0.017489218513047 +TR3788|c0_g1_i1 128.115824993653 24.010679388938 76.0632521912957 -1.20076602288383 0.555078500739638 -2.16323640941564 0.0305230012251409 0.0813946699337092 +TR1678|c0_g1_i1 0.695005959508731 7.10082184137838 3.89791390044355 1.13542782611345 0.54389306361848 2.08759387104432 0.0368344853417399 1 +TR1859|c3_g1_i1 0 2.05957798928713 1.02978899464357 1.08547672488113 0.52169423531112 2.08067609609255 0.0374635634690378 1 +TR1479|c0_g1_i1 353.92669362375 305.546165789569 329.736429706659 -0.210273055725041 0.101401657889395 -2.07366487000044 0.0381104459877385 0.0914650703705724 +TR1492|c0_g1_i2 1368.89238848897 813.514514376559 1091.20345143276 -0.673957173112486 0.33643480733027 -2.00323259790084 0.0451523282811554 0.0985141707952481 +TR2844|c0_g1_i1 220.566338218013 194.214843050373 207.390590634193 -0.1851823349888 0.101213323108161 -1.8296240979155 0.0673061677634479 0.134612335526896 +TR5075|c0_g1_i1 8.81552188359314 126.23137395943 67.5234479215117 0.86620707327725 0.498591364017662 1.73730861741634 0.0823327113057556 0.151998851641395 +TR2107|c1_g1_i1 7.08292121571621 1.78415791317121 4.43353956444371 -0.87765751535477 0.553196716703176 -1.58651974759584 0.112621456124343 1 +TR2672|c0_g1_i1 2.07518941673641 7.44710458698621 4.76114700186131 0.652733502871168 0.537764458916032 1.21379070715621 0.224827655823799 1 +TR4859|c0_g1_i1 3.10763825129944 1.1806627783491 2.14415051482427 -0.587630876626665 0.551071114588281 -1.06634309269812 0.28626857627862 1 +TR3091|c0_g1_i1 312.47018793986 293.531643106953 303.000915523406 -0.0879738435317154 0.0902971665647824 -0.97427025540829 0.329922369379669 0.501282895914669 +TR4163|c0_g1_i1 221.469120691076 207.118822998308 214.293971844692 -0.0959599050588562 0.0987561344325879 -0.97168551209707 0.331207026506115 0.501282895914669 +TR4669|c0_g2_i1 165.630009730314 0 82.8150048651569 -0.322459466822447 0.333908718519009 -0.965711432311973 0.334188597276446 0.501282895914669 +TR1894|c2_g1_i1 2.85762748931802 1.47338219762144 2.16550484346973 -0.426208431542948 0.551264679640795 -0.773146634064541 0.439435604855973 1 +TR3249|c0_g1_i1 2.06512931203634 4.15451161800812 3.10982046502223 0.3941103325595 0.539435464341514 0.730597742661558 0.465024891244583 1 +TR5212|c0_g1_i1 102.736339436612 86.4452993262187 94.5908193814151 -0.222704356323449 0.346653224187607 -0.642441324021618 0.520586675617895 0.734945894989969 +TR1122|c0_g1_i1 1.29006258579706 0.5946183773076 0.942340481552333 -0.302591524122929 0.512417527863229 -0.590517512905403 0.554843748171664 1 +TR2011|c5_g1_i1 7.597917075274 4.42090354598533 6.00941031062966 -0.246737820349972 0.517913150509813 -0.476407714511773 0.633783939711306 1 +TR1837|c2_g1_i1 2.16507864525674 1.46465683073113 1.81486773799393 -0.235474161889615 0.546181064177423 -0.431128388246582 0.666375020163124 1 +TR2182|c3_g2_i6 1.29006258579706 1.76655578876639 1.52830918728173 0.209843639881372 0.537581597903129 0.390347513195914 0.696279593847798 1 +TR1449|c0_g1_i1 98.9943307118646 106.843279101242 102.918804906553 0.100194141469895 0.276715374273995 0.362083753867198 0.717289443676285 0.9108498942696 +TR4277|c0_g1_i1 153.969096204861 149.159426886469 151.564261545665 -0.0459267760105497 0.128823197370029 -0.356510139075578 0.721458560376159 0.9108498942696 +TR1982|c2_g1_i1 5.5352448786851 10.687042573374 8.11114372602957 0.110416157924497 0.359967068804195 0.306739608962835 0.759041578558 0.9108498942696 +TR127|c1_g1_i1 1.20754470361908 1.49113571265046 1.34934020813477 0.142968860758062 0.541343527667515 0.26410006484066 0.791702813929264 1 +TR3854|c0_g1_i1 2260.55060252051 1927.46472630351 2094.00766441201 -0.135348942475858 0.546438760787258 -0.247692792291784 0.804372109047297 0.919282410339768 +TR2090|c0_g1_i1 9.46045896251181 5.6546754787973 7.55756722065455 -0.0586395744056909 0.302337767579782 -0.193953851267414 0.846212017000596 1 +TR3807|c0_g1_i1 0.347502979754365 0.292870809896544 0.320186894825454 -0.0640837282416973 0.445995787050203 -0.143686846608001 0.885747758296628 1 +TR131|c0_g1_i1 1275.67603302799 1312.2934796972 1293.9847563626 0.0343724958045096 0.405262489992082 0.0848153891695754 0.932408158838271 0.963782835492881 +TR5055|c0_g2_i1 5.17791343714095 5.60171771495863 5.38981557604979 0.043552763660028 0.53975688204026 0.0806895939805349 0.935688812631814 1 +TR939|c0_g1_i1 92.2508462008296 94.0990807885678 93.1749634946987 0.0253693962827489 0.353966153466169 0.0716718139130601 0.942863087697354 0.963782835492881 +TR2487|c0_g1_i1 875.181494043204 882.631049341941 878.906271692572 0.0115839334384507 0.255112918612705 0.0454070828770402 0.963782835492881 0.963782835492881
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,40 @@ +logFC logCPM PValue FDR +TR2779|c0_g1_i1 2.23948335958727 15.9163308249372 1.20766376889896e-237 4.70988869870595e-236 +TR1492|c0_g1_i2 -0.807859120941235 16.8439348559211 2.37986391219743e-61 4.64073462878498e-60 +TR1891|c0_g1_i1 1.35697452203657 14.6311197032228 1.60645028176433e-35 2.08838536629363e-34 +TR4761|c0_g1_i1 0.880921757190946 14.8138260614735 1.59143301924913e-24 1.5516471937679e-23 +TR2122|c0_g2_i2 0.729785350305026 14.7699678361852 6.52776857951534e-13 5.09165949202196e-12 +TR3854|c0_g1_i1 -0.289859344737128 17.7786469452325 6.1302236270955e-12 3.98464535761207e-11 +TR3638|c0_g1_i1 0.702510801497461 14.6355179638282 5.62335492840333e-11 3.133012031539e-10 +TR2278|c0_g1_i1 -0.490901034745758 15.2921454021456 1.53296499052609e-09 7.47320432881468e-09 +TR24|c0_g1_i1 2.16007337608378 13.5636496776551 8.67157466173412e-09 3.75768235341812e-08 +TR5075|c0_g1_i1 3.7524485458028 12.8683202800317 5.50095216588421e-08 2.14537134469484e-07 +TR4669|c0_g2_i1 -10.4044948993067 13.1110475123695 1.35189372056785e-06 4.79307773655872e-06 +TR3788|c0_g1_i1 -2.47698512550917 13.0240883091698 1.80487840553907e-05 5.86585481800198e-05 +TR1479|c0_g1_i1 -0.272661827455658 15.1172528121102 0.000483095512098729 0.00144928653629619 +TR1678|c0_g1_i1 3.02812287247775 9.36059212330112 0.0074853976481696 0.0208521791627582 +TR2107|c1_g1_i1 -1.98032359155541 9.36544178725855 0.0305238827180189 0.0756824353198294 +TR2844|c0_g1_i1 -0.244755727600329 14.4560017424587 0.0310492042337762 0.0756824353198294 +TR1859|c3_g1_i1 4.12978123132011 8.37588761488442 0.0428877609330621 0.0983895691993777 +TR3091|c0_g1_i1 -0.148576217250104 14.9963238698071 0.0547318692708507 0.11858571675351 +TR2672|c0_g1_i1 1.64029381826409 9.53984158811941 0.100507062957769 0.206303971334369 +TR4163|c0_g1_i1 -0.156926020788278 14.5006265631178 0.113620071038851 0.22155913852576 +TR4859|c0_g1_i1 -1.3062724221166 8.73091245897321 0.181160758857669 0.3364414093071 +TR4084|c0_g1_i1 0.390578563212142 13.8603174460746 0.270419882900116 0.479380701504752 +TR1982|c2_g1_i1 0.866592651710305 10.0958159836705 0.312186869456376 0.515984430920105 +TR1894|c2_g1_i1 -0.989932992780787 8.78384403630691 0.317528880566218 0.515984430920105 +TR4277|c0_g1_i1 -0.107189584823599 14.0046148411409 0.347278576725125 0.541754579691195 +TR2487|c0_g1_i1 -0.0467513454249246 16.526653433485 0.376403968202147 0.560230359736405 +TR3249|c0_g1_i1 1.00369455926223 9.08504250192555 0.387851787509819 0.560230359736405 +TR5212|c0_g1_i1 -0.310409394484433 13.3365591825697 0.416163942507532 0.572783249883747 +TR2011|c5_g1_i1 -0.799376994792807 9.70509536731836 0.425915749913555 0.572783249883747 +TR1837|c2_g1_i1 -0.59484087321072 8.66193471010726 0.588495494688377 0.76504414309489 +TR2090|c0_g1_i1 -0.766971023107968 9.89421471118339 0.638322407555079 0.8030507707951 +TR131|c0_g1_i1 -0.0187996511046741 17.0827735361623 0.697507705031756 0.850087515507453 +TR1122|c0_g1_i1 -0.908051089281089 8.22928258978683 0.753364106379395 0.890339398448377 +TR1449|c0_g1_i1 0.0452741219590205 13.4583026590017 0.919111339143084 1 +TR939|c0_g1_i1 -0.0309689709592036 13.3146949564453 0.956245904999637 1 +TR5055|c0_g2_i1 0.0548476287872344 9.62768102188797 0.999999999999985 1 +TR2182|c3_g2_i6 0.517423422896207 8.5297276065799 1 1 +TR127|c1_g1_i1 0.299043611515333 8.4576897025083 1 1 +TR3807|c0_g1_i1 -0.266132577378544 7.94319410024963 1 1
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,40 @@ +logFC logCPM PValue FDR +TR2779|c0_g1_i1 2.23795519272237 15.9076254017254 2.92187316761645e-09 1.13953053537042e-07 +TR1492|c0_g1_i2 -0.807554446371668 16.8426446227048 5.58321346448906e-08 1.08872662557537e-06 +TR24|c0_g1_i1 2.16839334936064 13.5222768601527 3.73856822091501e-07 4.86013868718952e-06 +TR3788|c0_g1_i1 -2.47096654484901 13.0144557887788 1.245732049043e-06 9.71670998253539e-06 +TR5075|c0_g1_i1 3.68481140303272 12.7944067233298 3.44359702134355e-06 2.23833806387331e-05 +TR3854|c0_g1_i1 -0.290746293924475 17.7782076349597 5.25322144866517e-07 5.12189091244854e-06 +TR1891|c0_g1_i1 1.35768165107067 14.6117632515968 5.28666359293828e-06 2.79053243123467e-05 +TR4761|c0_g1_i1 0.878920056028248 14.8002262876656 5.72416908971214e-06 2.79053243123467e-05 +TR2122|c0_g2_i2 0.730166040402744 14.7551588447381 0.000213340170514583 0.000924474072229861 +TR3638|c0_g1_i1 0.708321413581678 14.6195575978943 0.000258928735946659 0.00100982207019197 +TR2107|c1_g1_i1 -1.90861736829884 8.90712643491077 0.00457979737107378 0.0148843414559898 +TR1678|c0_g1_i1 2.86408187112217 8.67828416118206 0.00614682516189 0.01844047548567 +TR2278|c0_g1_i1 -0.503051556783977 15.2850549214884 0.00155857674629228 0.00552586300958173 +TR1859|c3_g1_i1 1.96144637998691 6.77065030795652 0.0428269385052548 0.0982500353944082 +TR2672|c0_g1_i1 1.69730734417424 8.97832173338033 0.0866262290356731 0.160877282494822 +TR1479|c0_g1_i1 -0.277933522953326 15.1098597149167 0.0157877120065803 0.0439800548754737 +TR1982|c2_g1_i1 0.859948395691952 9.74982883974683 0.0845253825418736 0.160877282494822 +TR4859|c0_g1_i1 -1.04376243585308 7.84838377560073 0.178339170085147 0.289801151388364 +TR2011|c5_g1_i1 -0.835627288758852 9.33803398810951 0.117576176969539 0.20843049553691 +TR4084|c0_g1_i1 0.383433512314591 13.8345091917852 0.0320674039619619 0.083375250301101 +TR1894|c2_g1_i1 -0.899367664455804 7.86698528437277 0.236693956821629 0.369242572641742 +TR5212|c0_g1_i1 -0.317453614519532 13.3093804544918 0.0408068910563242 0.0982500353944082 +TR2182|c3_g2_i6 0.988859576038597 7.34392475064937 0.332144974966109 0.462630500845651 +TR3249|c0_g1_i1 1.18548803762213 8.36747688877935 0.296376188714782 0.444564283072173 +TR1837|c2_g1_i1 -0.83411458992077 7.6102620160458 0.393260306376011 0.528867308574635 +TR3807|c0_g1_i1 -0.40219136988549 5.09566487188118 0.681998347783062 0.765740423023185 +TR4669|c0_g2_i1 -6.05037553674292 13.1239272719772 0.480074268471172 0.603964402270185 +TR1122|c0_g1_i1 -0.184244267394782 6.64199260311611 0.869699168726351 0.892585988955992 +TR127|c1_g1_i1 0.354388761220407 7.15556768591471 0.687202943738756 0.765740423023185 +TR2844|c0_g1_i1 -0.251980888130202 14.4425124782726 0.0594765231313145 0.128865800117848 +TR2090|c0_g1_i1 0.862128177746631 9.64998833298881 0.646749723219784 0.764340581987017 +TR3091|c0_g1_i1 -0.148831558112849 14.9878570236746 0.0841354210369957 0.160877282494822 +TR5055|c0_g2_i1 -0.0583511298028353 9.18288041060754 0.918331019801174 0.918331019801174 +TR4163|c0_g1_i1 -0.161834057105857 14.4879250602579 0.126768900432688 0.214955961603254 +TR4277|c0_g1_i1 -0.103273026252208 13.9874746529507 0.30829078508145 0.445308911784317 +TR939|c0_g1_i1 -0.0333503331526365 13.2856573711711 0.715260879184748 0.774865952450143 +TR1449|c0_g1_i1 0.049884213852527 13.4293306544833 0.75234222467997 0.793009371959969 +TR2487|c0_g1_i1 -0.0480185034754555 16.5239765307922 0.407818984620182 0.530164680006236 +TR131|c0_g1_i1 -0.0203187870937255 17.0810493411762 0.539920494505425 0.658028102678487
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/express_bowtie/results.xprs Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ +bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm +1 TRINITY_DN2_c3_g1_i1 202 0.000000 0 0 0.000000 0.000000 0.000000e00 0.000000e00 0.000000e00 0.000000e00 0.000000e00 F 0.000000e+00 +2 TRINITY_DN1_c0_g1_i1 380 109.247050 5 5 5.000000 17.391774 0.000000e00 0.000000e00 4.160711e06 4.160711e06 4.160711e06 T 6.610131e+05 +3 TRINITY_DN2_c0_g1_i1 279 0.000000 0 0 0.000000 0.000000 0.000000e00 0.000000e00 0.000000e00 0.000000e00 0.000000e00 F 0.000000e+00 +4 TRINITY_DN0_c0_g1_i1 229 0.000000 0 0 0.000000 0.000000 0.000000e00 0.000000e00 0.000000e00 0.000000e00 0.000000e00 F 0.000000e+00 +5 TRINITY_DN2_c1_g1_i1 541 259.008053 5 5 5.000000 10.443691 0.000000e00 0.000000e00 1.754947e06 1.754947e06 1.754947e06 T 2.788088e+05 +6 TRINITY_DN2_c2_g1_i1 240 240.000000 1 1 1.000000 1.000000 0.000000e00 0.000000e00 3.787879e05 3.787879e05 3.787879e05 T 6.017811e+04 +7 TRINITY_DN3_c0_g1_i1 216 0.000000 0 0 0.000000 0.000000 0.000000e00 0.000000e00 0.000000e00 0.000000e00 0.000000e00 F 0.000000e+00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/express_bowtie/results_B.xprs Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ +bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm +1 TRINITY_DN0_c0_g1_i1 380 109.247050 5 5 5.000000 17.391774 0.000000e+00 0.000000e+00 4.160711e+06 4.160711e+06 4.160711e+06 T 6.610131e+05 +2 TRINITY_DN2_c0_g1_i1 279 0.000000 0 0 0.000000 0.000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 F 0.000000e+00 +3 TRINITY_DN2_c1_g1_i1 240 240.000000 1 1 1.000000 1.000000 0.000000e+00 0.000000e+00 3.787879e+05 3.787879e+05 3.787879e+05 T 6.017811e+04 +4 TRINITY_DN1_c0_g1_i1 229 0.000000 0 0 0.000000 0.000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 F 0.000000e+00 +5 TRINITY_DN3_c0_g1_i1 216 0.000000 0 0 0.000000 0.000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 F 0.000000e+00 +6 TRINITY_DN2_c3_g1_i1 202 0.000000 0 0 0.000000 0.000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 F 0.000000e+00 +7 TRINITY_DN2_c2_g1_i1 541 259.008053 5 5 5.000000 10.443691 0.000000e+00 0.000000e+00 1.754947e+06 1.754947e+06 1.754947e+06 T 2.788088e+05
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/express_bowtie/sample_A Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ +bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm +NA TRINITY_DN3_c0_g1 216.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN2_c2_g1 240.00 240.00 NA NA NA 1.00 NA NA 378787.90 NA NA NA 60178.11 +NA TRINITY_DN2_c3_g1 202.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN0_c0_g1 229.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN2_c0_g1 279.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN1_c0_g1 380.00 109.25 NA NA NA 17.39 NA NA 4160711.00 NA NA NA 661013.1 +NA TRINITY_DN2_c1_g1 541.00 259.01 NA NA NA 10.44 NA NA 1754947.00 NA NA NA 278808.8
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/express_bowtie/sample_B Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ +bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm +NA TRINITY_DN3_c0_g1 216.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN2_c1_g1 240.00 240.00 NA NA NA 1.00 NA NA 378787.90 NA NA NA 60178.11 +NA TRINITY_DN2_c3_g1 202.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN0_c0_g1 380.00 109.25 NA NA NA 17.39 NA NA 4160711.00 NA NA NA 661013.1 +NA TRINITY_DN1_c0_g1 229.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN2_c0_g1 279.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN2_c2_g1 541.00 259.01 NA NA NA 10.44 NA NA 1754947.00 NA NA NA 278808.8
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_express_bowtie/matrix.TMM.EXPR.matrix Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN2_c1_g1_i1 278808.8 60178.11 +TRINITY_DN1_c0_g1_i1 0 0 +TRINITY_DN2_c2_g1_i1 60178.11 278808.8 +TRINITY_DN2_c0_g1_i1 0 0 +TRINITY_DN3_c0_g1_i1 0 0 +TRINITY_DN2_c3_g1_i1 0 0 +TRINITY_DN0_c0_g1_i1 661013.1 661013.1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_express_bowtie/matrix.TPM.not_cross_norm Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN2_c1_g1_i1 278808.8 60178.11 +TRINITY_DN1_c0_g1_i1 0 0 +TRINITY_DN2_c2_g1_i1 60178.11 278808.8 +TRINITY_DN2_c0_g1_i1 0 0 +TRINITY_DN3_c0_g1_i1 0 0 +TRINITY_DN2_c3_g1_i1 0 0 +TRINITY_DN0_c0_g1_i1 661013.1 661013.1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_express_bowtie/matrix.counts.matrix Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN2_c1_g1_i1 10.443691 1.000000 +TRINITY_DN1_c0_g1_i1 0.000000 0.000000 +TRINITY_DN2_c2_g1_i1 1.000000 10.443691 +TRINITY_DN2_c0_g1_i1 0.000000 0.000000 +TRINITY_DN3_c0_g1_i1 0.000000 0.000000 +TRINITY_DN2_c3_g1_i1 0.000000 0.000000 +TRINITY_DN0_c0_g1_i1 17.391774 17.391774
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie/matrix.TMM.EXPR.matrix Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN3_c0_g1 0 0 +TRINITY_DN4_c0_g1 0 0 +TRINITY_DN0_c0_g1 331152.79 331152.79 +TRINITY_DN2_c0_g1 0 0 +TRINITY_DN3_c2_g1 524034.76 144812.45 +TRINITY_DN3_c1_g1 144812.45 524034.76 +TRINITY_DN3_c3_g1 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie/matrix.TPM.not_cross_norm Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN3_c0_g1 0 0 +TRINITY_DN4_c0_g1 0 0 +TRINITY_DN0_c0_g1 331152.79 331152.79 +TRINITY_DN2_c0_g1 0 0 +TRINITY_DN3_c2_g1 524034.76 144812.45 +TRINITY_DN3_c1_g1 144812.45 524034.76 +TRINITY_DN3_c3_g1 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie/matrix.counts.matrix Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN3_c0_g1 0.00 0.00 +TRINITY_DN4_c0_g1 0.00 0.00 +TRINITY_DN0_c0_g1 5.00 5.00 +TRINITY_DN2_c0_g1 0.00 0.00 +TRINITY_DN3_c2_g1 1.00 5.00 +TRINITY_DN3_c1_g1 5.00 1.00 +TRINITY_DN3_c3_g1 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie2/matrix.TMM.EXPR.matrix Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN3_c0_g1 0 0 +TRINITY_DN2_c2_g1 529174.03 161779.66 +TRINITY_DN2_c3_g1 0 0 +TRINITY_DN0_c0_g1 309046.31 309046.31 +TRINITY_DN2_c0_g1 0 0 +TRINITY_DN1_c0_g1 0 0 +TRINITY_DN2_c1_g1 161779.66 529174.03
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie2/matrix.TPM.not_cross_norm Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN3_c0_g1 0 0 +TRINITY_DN2_c2_g1 529174.03 161779.66 +TRINITY_DN2_c3_g1 0 0 +TRINITY_DN0_c0_g1 309046.31 309046.31 +TRINITY_DN2_c0_g1 0 0 +TRINITY_DN1_c0_g1 0 0 +TRINITY_DN2_c1_g1 161779.66 529174.03
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie2/matrix.counts.matrix Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN3_c0_g1 0.00 0.00 +TRINITY_DN2_c2_g1 1.00 6.00 +TRINITY_DN2_c3_g1 0.00 0.00 +TRINITY_DN0_c0_g1 5.00 5.00 +TRINITY_DN2_c0_g1 0.00 0.00 +TRINITY_DN1_c0_g1 0.00 0.00 +TRINITY_DN2_c1_g1 6.00 1.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN3_c0_g1 0 0 +TRINITY_DN4_c0_g1 0 0 +TRINITY_DN0_c0_g1 331152.79 331152.79 +TRINITY_DN2_c0_g1 0 0 +TRINITY_DN3_c2_g1 524034.76 144812.45 +TRINITY_DN3_c1_g1 144812.45 524034.76 +TRINITY_DN3_c3_g1 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm.upper_quartile_norm.matrix Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ +RSEM RSEM.isoforms_B.results +TRINITY_DN3_c2_g1_i1 524034.76 144812.45 +TRINITY_DN4_c0_g1_i1 0 0 +TRINITY_DN3_c3_g1_i1 0 0 +TRINITY_DN3_c1_g1_i1 144812.45 524034.76 +TRINITY_DN2_c0_g1_i1 0 0 +TRINITY_DN3_c0_g1_i1 0 0 +TRINITY_DN0_c0_g1_i1 331152.79 331152.79
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.UpperQuartile.EXPR.matrix Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ +sample_A sample_B +TRINITY_DN2_c0_g1 0 0 +TRINITY_DN1_c0_g1 329523.81 329523.81 +TRINITY_DN0_c0_g1 0 0 +TRINITY_DN2_c1_g1 145165.14 525311.05 +TRINITY_DN3_c0_g1 0 0 +TRINITY_DN2_c2_g1 525311.05 145165.14 +TRINITY_DN2_c3_g1 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.counts.matrix Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN3_c0_g1 0.00 0.00 +TRINITY_DN4_c0_g1 0.00 0.00 +TRINITY_DN0_c0_g1 5.00 5.00 +TRINITY_DN2_c0_g1 0.00 0.00 +TRINITY_DN3_c2_g1 1.00 5.00 +TRINITY_DN3_c1_g1 5.00 1.00 +TRINITY_DN3_c3_g1 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie_none/matrix.TPM.not_cross_norm Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN3_c0_g1 0 0 +TRINITY_DN4_c0_g1 0 0 +TRINITY_DN0_c0_g1 331152.79 331152.79 +TRINITY_DN2_c0_g1 0 0 +TRINITY_DN3_c2_g1 524034.76 144812.45 +TRINITY_DN3_c1_g1 144812.45 524034.76 +TRINITY_DN3_c3_g1 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie_none/matrix.counts.matrix Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN3_c0_g1 0.00 0.00 +TRINITY_DN4_c0_g1 0.00 0.00 +TRINITY_DN0_c0_g1 5.00 5.00 +TRINITY_DN2_c0_g1 0.00 0.00 +TRINITY_DN3_c2_g1 1.00 5.00 +TRINITY_DN3_c1_g1 5.00 1.00 +TRINITY_DN3_c3_g1 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/qcheck/matrix.counts.matrix Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,41 @@ + wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR24|c0_g1_i1 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00 +TR2779|c0_g1_i1 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00 +TR127|c1_g1_i1 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 +TR2107|c1_g1_i1 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00 +TR2011|c5_g1_i1 11.00 4.00 4.00 8.00 5.00 7.00 3.00 4.00 8.00 +TR4163|c0_g1_i1 368.00 422.00 425.00 172.00 216.00 210.00 234.00 254.00 212.00 +TR5055|c0_g2_i1 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00 +TR1449|c0_g1_i1 196.00 230.00 207.00 66.00 113.00 91.00 124.00 130.00 107.00 +TR1982|c2_g1_i1 7.00 7.00 6.00 4.00 3.00 8.00 16.00 9.00 11.00 +TR1859|c3_g1_i1 0.00 0.00 1.00 0.00 0.00 0.00 1.00 2.00 4.00 +TR1492|c0_g1_i2 1895.00 1906.00 1921.00 1104.00 1263.00 1319.00 899.00 929.00 922.00 +TR1122|c0_g1_i1 2.00 3.00 0.00 3.00 0.00 0.00 1.00 1.00 0.00 +TR2278|c0_g1_i1 497.00 610.00 598.00 333.00 406.00 413.00 323.00 409.00 337.00 +TR4084|c0_g1_i1 95.00 148.00 86.00 77.00 111.00 127.00 175.00 201.00 158.00 +TR4761|c0_g1_i1 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00 +TR3638|c0_g1_i1 647.00 676.00 712.00 117.00 184.00 174.00 324.00 344.00 338.00 +TR2090|c0_g1_i1 0.00 0.00 0.00 22.00 0.00 0.02 10.33 0.00 9.09 +TR3854|c0_g1_i1 1878.00 1734.00 1864.00 1775.00 2173.00 2151.00 2216.00 2142.00 2155.00 +TR131|c0_g1_i1 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00 +TR5075|c0_g1_i1 13.00 22.00 21.00 6.00 8.00 10.00 163.00 121.00 142.00 +TR2182|c3_g2_i6 1.44 2.70 3.84 3.35 0.00 0.00 1.22 2.18 2.63 +TR3788|c0_g1_i1 17.00 30.00 22.00 91.00 132.00 125.00 32.00 22.00 27.00 +TR4859|c0_g1_i1 6.00 12.00 8.00 4.00 1.00 3.00 1.00 1.00 2.00 +TR2487|c0_g1_i1 386.00 383.00 424.00 689.00 866.00 806.00 963.00 989.00 1032.00 +TR2122|c0_g2_i2 145.00 135.00 136.00 155.00 157.00 201.00 369.00 398.00 344.00 +TR4277|c0_g1_i1 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00 +TR4669|c0_g2_i1 0.00 0.00 0.00 209.00 0.00 217.50 0.14 0.06 0.18 +TR3091|c0_g1_i1 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00 +TR2130|c1_g3_i1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 +TR3807|c0_g1_i1 6.00 4.00 2.00 0.00 0.00 1.00 0.00 1.00 0.00 +TR1894|c2_g1_i1 21.00 14.00 11.00 1.00 2.00 5.00 1.00 3.00 1.00 +TR5212|c0_g1_i1 64.00 89.00 78.00 73.00 98.00 108.00 103.00 105.00 84.00 +TR939|c0_g1_i1 96.00 99.00 99.00 72.00 89.00 88.00 107.00 103.00 108.00 +TR1891|c0_g1_i1 115.00 137.96 124.00 96.53 139.00 110.94 364.77 411.00 384.00 +TR2672|c0_g1_i1 14.00 29.00 22.00 0.00 4.00 2.00 14.00 4.00 7.00 +TR2844|c0_g1_i1 166.00 211.00 178.00 161.00 214.00 223.00 199.00 245.00 213.00 +TR1837|c2_g1_i1 1.00 0.00 0.00 1.00 1.00 4.00 0.00 3.00 2.00 +TR1678|c0_g1_i1 1.00 0.00 1.00 0.00 0.00 2.00 8.00 10.00 6.00 +TR3249|c0_g1_i1 1.00 2.00 1.00 4.00 1.00 0.00 6.00 1.00 7.00 +TR1479|c0_g1_i1 136.00 178.00 141.00 277.00 324.00 354.00 367.00 363.00 302.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie/RSEM.isoforms.results Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ +transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct +TRINITY_DN0_c0_g1_i1 TRINITY_DN0_c0_g1 229 11.55 0.00 0.00 0.00 0.00 +TRINITY_DN1_c0_g1_i1 TRINITY_DN1_c0_g1 380 123.91 5.00 329523.81 3668378.58 100.00 +TRINITY_DN2_c0_g1_i1 TRINITY_DN2_c0_g1 279 35.45 0.00 0.00 0.00 0.00 +TRINITY_DN2_c1_g1_i1 TRINITY_DN2_c1_g1 541 281.27 5.00 145165.14 1616031.03 100.00 +TRINITY_DN2_c2_g1_i1 TRINITY_DN2_c2_g1 240 15.55 1.00 525311.05 5847953.22 100.00 +TRINITY_DN2_c3_g1_i1 TRINITY_DN2_c3_g1 202 3.45 0.00 0.00 0.00 0.00 +TRINITY_DN3_c0_g1_i1 TRINITY_DN3_c0_g1 216 6.82 0.00 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie/RSEM.isoforms_B.results Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ +transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct +TRINITY_DN0_c0_g1_i1 TRINITY_DN0_c0_g1 229 11.55 0.00 0.00 0.00 0.00 +TRINITY_DN1_c0_g1_i1 TRINITY_DN1_c0_g1 380 123.91 5.00 329523.81 3668378.58 100.00 +TRINITY_DN2_c0_g1_i1 TRINITY_DN2_c0_g1 279 35.45 0.00 0.00 0.00 0.00 +TRINITY_DN2_c2_g1_i1 TRINITY_DN2_c2_g1 541 281.27 5.00 145165.14 1616031.03 100.00 +TRINITY_DN2_c1_g1_i1 TRINITY_DN2_c1_g1 240 15.55 1.00 525311.05 5847953.22 100.00 +TRINITY_DN2_c3_g1_i1 TRINITY_DN2_c3_g1 202 3.45 0.00 0.00 0.00 0.00 +TRINITY_DN3_c0_g1_i1 TRINITY_DN3_c0_g1 216 6.82 0.00 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie/sample_A Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 11.55 0.00 0.00 0.00 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 123.91 5.00 329523.81 3668378.58 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 35.45 0.00 0.00 0.00 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 541.00 281.27 5.00 145165.14 1616031.03 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 240.00 15.55 1.00 525311.05 5847953.22 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.45 0.00 0.00 0.00 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.82 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie/sample_B Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 11.55 0.00 0.00 0.00 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 123.91 5.00 329523.81 3668378.58 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 35.45 0.00 0.00 0.00 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 541.00 281.27 5.00 145165.14 1616031.03 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 240.00 15.55 1.00 525311.05 5847953.22 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.45 0.00 0.00 0.00 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.82 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie2/RSEM.isoforms.results Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ +transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct +TRINITY_DN0_c0_g1_i1 TRINITY_DN0_c0_g1 229 10.58 0.00 0.00 0.00 0.00 +TRINITY_DN1_c0_g1_i1 TRINITY_DN1_c0_g1 380 122.00 5.00 309046.31 3415300.55 100.00 +TRINITY_DN2_c0_g1_i1 TRINITY_DN2_c0_g1 279 32.50 0.00 0.00 0.00 0.00 +TRINITY_DN2_c1_g1_i1 TRINITY_DN2_c1_g1 541 279.67 6.00 161779.66 1787842.67 100.00 +TRINITY_DN2_c2_g1_i1 TRINITY_DN2_c2_g1 240 14.25 1.00 529174.03 5847953.22 100.00 +TRINITY_DN2_c3_g1_i1 TRINITY_DN2_c3_g1 202 3.17 0.00 0.00 0.00 0.00 +TRINITY_DN3_c0_g1_i1 TRINITY_DN3_c0_g1 216 6.25 0.00 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie2/RSEM.isoforms_B.results Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ +transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct +TRINITY_DN0_c0_g1_i1 TRINITY_DN0_c0_g1 380 122.00 5.00 309046.31 3415300.55 100.00 +TRINITY_DN1_c0_g1_i1 TRINITY_DN1_c0_g1 229 10.58 0.00 0.00 0.00 0.00 +TRINITY_DN2_c0_g1_i1 TRINITY_DN2_c0_g1 279 32.50 0.00 0.00 0.00 0.00 +TRINITY_DN2_c2_g1_i1 TRINITY_DN2_c2_g1 541 279.67 6.00 161779.66 1787842.67 100.00 +TRINITY_DN2_c1_g1_i1 TRINITY_DN2_c1_g1 240 14.25 1.00 529174.03 5847953.22 100.00 +TRINITY_DN2_c3_g1_i1 TRINITY_DN2_c3_g1 202 3.17 0.00 0.00 0.00 0.00 +TRINITY_DN3_c0_g1_i1 TRINITY_DN3_c0_g1 216 6.25 0.00 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie2/sample_A Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 10.58 0.00 0.00 0.00 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 122.00 5.00 309046.31 3415300.55 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 32.50 0.00 0.00 0.00 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 541.00 279.67 6.00 161779.66 1787842.67 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 240.00 14.25 1.00 529174.03 5847953.22 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.17 0.00 0.00 0.00 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.25 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie2/sample_B Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 380.00 122.00 5.00 309046.31 3415300.55 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 229.00 10.58 0.00 0.00 0.00 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 32.50 0.00 0.00 0.00 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 541.00 279.67 6.00 161779.66 1787842.67 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 240.00 14.25 1.00 529174.03 5847953.22 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.17 0.00 0.00 0.00 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.25 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/salmon/sample_A Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ +Name Length EffectiveLength TPM NumReads +TRINITY_DN1_c0_g1_i1 380 120.403 179183 13 +TRINITY_DN0_c0_g1_i1 229 229 55271.5 7.62686 +TRINITY_DN2_c0_g1_i1 279 31.1522 565494 10.6151 +TRINITY_DN2_c1_g1_i1 541 278.129 113370 19 +TRINITY_DN2_c2_g1_i1 240 240 32900.7 4.75801 +TRINITY_DN2_c3_g1_i1 202 202 0 0 +TRINITY_DN3_c0_g1_i1 216 216 53781.8 7
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/salmon/sample_B Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ +Name Length EffectiveLength TPM NumReads +TRINITY_DN2_c2_g1 240.00 240.00 32900.70 4.76 +TRINITY_DN0_c0_g1 229.00 229.00 55271.50 7.63 +TRINITY_DN1_c0_g1 380.00 120.40 179183.00 13.00 +TRINITY_DN2_c0_g1 279.00 31.15 565494.00 10.62 +TRINITY_DN2_c3_g1 202.00 202.00 0.00 0.00 +TRINITY_DN3_c0_g1 216.00 216.00 53781.80 7.00 +TRINITY_DN2_c1_g1 541.00 278.13 113370.00 19.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/samples.txt Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,9 @@ +wt_37 wt_37_1 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_1-SRX707647-SRR1582649_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_1-SRX707647-SRR1582649_2.fastq +wt_37 wt_37_2 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_2-SRX707648-SRR1582650_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_2-SRX707648-SRR1582650_2.fastq +wt_37 wt_37_3 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_3-SRX707649-SRR1582651_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_3-SRX707649-SRR1582651_2.fastq +wt_GSNO wt_GSNO_1 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_1-SRX707644-SRR1582646_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_1-SRX707644-SRR1582646_2.fastq +wt_GSNO wt_GSNO_2 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_2-SRX707645-SRR1582647_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_2-SRX707645-SRR1582647_2.fastq +wt_GSNO wt_GSNO_3 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_3-SRX707646-SRR1582648_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_3-SRX707646-SRR1582648_2.fastq +wt_ph8 wt_ph8_1 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_1-SRX707641-SRR1582643_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_1-SRX707641-SRR1582643_2.fastq +wt_ph8 wt_ph8_2 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_2-SRX707642-SRR1582644_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_2-SRX707642-SRR1582644_2.fastq +wt_ph8 wt_ph8_3 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_3-SRX707643-SRR1582645_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_3-SRX707643-SRR1582645_2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/trinotate/genes.lengths.txt Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,40 @@ +gene_id length +TR24|c0_g1_i1 290.00 +TR2779|c0_g1_i1 186.00 +TR127|c1_g1_i1 229.00 +TR2107|c1_g1_i1 259.00 +TR2011|c5_g1_i1 211.00 +TR4163|c0_g1_i1 368.00 +TR5055|c0_g2_i1 236.00 +TR1449|c0_g1_i1 196.00 +TR1982|c2_g1_i1 227.00 +TR1859|c3_g1_i1 220.00 +TR1492|c0_g1_i2 195.00 +TR1122|c0_g1_i1 222.00 +TR2278|c0_g1_i1 497.00 +TR4084|c0_g1_i1 295.00 +TR4761|c0_g1_i1 289.00 +TR3638|c0_g1_i1 247.00 +TR2090|c0_g1_i1 220.00 +TR3854|c0_g1_i1 178.00 +TR131|c0_g1_i1 232.00 +TR5075|c0_g1_i1 213.00 +TR2182|c3_g2_i6 221.44 +TR3788|c0_g1_i1 217.00 +TR4859|c0_g1_i1 226.00 +TR2487|c0_g1_i1 386.00 +TR2122|c0_g2_i2 145.00 +TR4277|c0_g1_i1 466.00 +TR3091|c0_g1_i1 222.00 +TR2130|c1_g3_i1 220.00 +TR3807|c0_g1_i1 226.00 +TR1894|c2_g1_i1 221.00 +TR5212|c0_g1_i1 264.00 +TR939|c0_g1_i1 296.00 +TR1891|c0_g1_i1 115.00 +TR2672|c0_g1_i1 214.00 +TR2844|c0_g1_i1 166.00 +TR1837|c2_g1_i1 221.00 +TR1678|c0_g1_i1 221.00 +TR3249|c0_g1_i1 221.00 +TR1479|c0_g1_i1 136.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/trinotate/go_annotations.txt Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,39 @@ +TR24|c0_g1_i1 GO:0003674,GO:0003824,GO:0003865,GO:0005575,GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229,GO:0016491,GO:0016627,GO:0031090,GO:0033765,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0071704,GO:0098588,GO:0098589,GO:1901360 +TR2779|c0_g1_i1 GO:0003674,GO:0003824,GO:0004596,GO:0005575,GO:0005634,GO:0005737,GO:0008080,GO:0016407,GO:0016410,GO:0016740,GO:0016746,GO:0016747,GO:0034212,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464 +TR127|c1_g1_i1 GO:0003674,GO:0003824,GO:0004310,GO:0004311,GO:0004659,GO:0005575,GO:0005789,GO:0006066,GO:0006629,GO:0006694,GO:0006720,GO:0008150,GO:0008152,GO:0008202,GO:0008299,GO:0008610,GO:0009058,GO:0009987,GO:0016020,GO:0016021,GO:0016125,GO:0016126,GO:0016491,GO:0016740,GO:0016765,GO:0031090,GO:0044237,GO:0044238,GO:0044249,GO:0044255,GO:0044281,GO:0044283,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0044711,GO:0044763,GO:0046165,GO:0051996,GO:0071704,GO:0098588,GO:0098589,GO:1901360,GO:1901362,GO:1901576,GO:1901615,GO:1901617 +TR2107|c1_g1_i1 GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175,GO:0004190,GO:0004518,GO:0004519,GO:0005488,GO:0006139,GO:0006259,GO:0006310,GO:0006725,GO:0006807,GO:0008150,GO:0008152,GO:0008233,GO:0009987,GO:0015074,GO:0016740,GO:0016772,GO:0016779,GO:0016787,GO:0016788,GO:0034061,GO:0034641,GO:0043167,GO:0043169,GO:0043170,GO:0044237,GO:0044238,GO:0044260,GO:0046483,GO:0046872,GO:0070001,GO:0070011,GO:0071704,GO:0090304,GO:0097159,GO:1901360,GO:1901363 +TR2011|c5_g1_i1 GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005737,GO:0006801,GO:0006810,GO:0006811,GO:0006812,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169,GO:0044237,GO:0044424,GO:0044464,GO:0044699,GO:0044710,GO:0044765,GO:0046872,GO:0046914,GO:0051234,GO:0055114,GO:0072593 +TR4163|c0_g1_i1 GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005634,GO:0005743,GO:0005829,GO:0006801,GO:0006873,GO:0006875,GO:0006878,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0010035,GO:0010038,GO:0016020,GO:0016530,GO:0016531,GO:0016532,GO:0019725,GO:0019866,GO:0030003,GO:0030234,GO:0031090,GO:0031966,GO:0042221,GO:0042592,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044237,GO:0044422,GO:0044424,GO:0044429,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0044763,GO:0046872,GO:0046914,GO:0046916,GO:0048878,GO:0050801,GO:0050896,GO:0051716,GO:0055065,GO:0055070,GO:0055076,GO:0055080,GO:0055082,GO:0055114,GO:0065007,GO:0065008,GO:0070887,GO:0071241,GO:0071248,GO:0072593 +TR5055|c0_g2_i1 GO:0003674,GO:0005488,GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872,GO:0046914 +TR1449|c0_g1_i1 GO:0003674,GO:0005488,GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872,GO:0046914 +TR1982|c2_g1_i1 GO:0003674,GO:0003824,GO:0003865,GO:0005575,GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229,GO:0016491,GO:0016627,GO:0031090,GO:0033765,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0071704,GO:0098588,GO:0098589,GO:1901360 +TR1859|c3_g1_i1 GO:0003676 +TR1492|c0_g1_i2 GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229 +TR1122|c0_g1_i1 GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234 +TR2278|c0_g1_i1 GO:0031090,GO:0033765 +TR4084|c0_g1_i1 GO:0003674,GO:0005488,GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872,GO:0046914 +TR4761|c0_g1_i1 GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234 +TR3638|c0_g1_i1 GO:0003865,GO:0005575,GO:0005783 +TR2090|c0_g1_i1 GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005634,GO:0005743,GO:0005829,GO:0006801,GO:0006873,GO:0006875,GO:0006878,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0010035,GO:0010038,GO:0016020,GO:0016530,GO:0016531,GO:0016532,GO:0019725,GO:0019866,GO:0030003,GO:0030234,GO:0031090,GO:0031966,GO:0042221,GO:0042592,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044237,GO:0044422,GO:0044424,GO:0044429,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0044763,GO:0046872,GO:0046914,GO:0046916,GO:0048878,GO:0050801,GO:0050896,GO:0051716,GO:0055065,GO:0055070,GO:0055076,GO:0055080,GO:0055082,GO:0055114,GO:0065007,GO:0065008,GO:0070887,GO:0071241,GO:0071248,GO:0072593 +TR3854|c0_g1_i1 GO:0003674,GO:0003824,GO:0003865,GO:0005575,GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229,GO:0016491,GO:0016627,GO:0031090,GO:0033765,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0071704,GO:0098588,GO:0098589,GO:1901360 +TR131|c0_g1_i1 GO:0031090,GO:0033765 +TR5075|c0_g1_i1 GO:0031090,GO:0033765 +TR2182|c3_g2_i6 GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175,GO:0004190,GO:0004518,GO:0004519,GO:0005488,GO:0006139 +TR3788|c0_g1_i1 GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229 +TR4859|c0_g1_i1 GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175,GO:0004190,GO:0004518,GO:0004519,GO:0005488,GO:0006139 +TR2487|c0_g1_i1 GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169 +TR2122|c0_g2_i2 GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872 +TR4277|c0_g1_i1 GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872 +TR3091|c0_g1_i1 GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169 +TR2130|c1_g3_i1 GO:0003674,GO:0003824,GO:0003865,GO:0005575,GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229,GO:0016491,GO:0016627,GO:0031090,GO:0033765,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0071704,GO:0098588,GO:0098589,GO:1901360 +TR3807|c0_g1_i1 GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005634,GO:0005743,GO:0005829,GO:0006801,GO:0006873,GO:0006875,GO:0006878,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0010035,GO:0010038,GO:0016020,GO:0016530,GO:0016531,GO:0016532,GO:0019725,GO:0019866,GO:0030003,GO:0030234,GO:0031090,GO:0031966,GO:0042221,GO:0042592,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044237,GO:0044422,GO:0044424,GO:0044429,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0044763,GO:0046872,GO:0046914,GO:0046916,GO:0048878,GO:0050801,GO:0050896,GO:0051716,GO:0055065,GO:0055070,GO:0055076,GO:0055080,GO:0055082,GO:0055114,GO:0065007,GO:0065008,GO:0070887,GO:0071241,GO:0071248,GO:0072593 +TR1894|c2_g1_i1 GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872 +TR5212|c0_g1_i1 GO:0003865,GO:0005575,GO:0005783 +TR939|c0_g1_i1 GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175,GO:0004190,GO:0004518,GO:0004519,GO:0005488,GO:0006139 +TR1891|c0_g1_i1 GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175 +TR2672|c0_g1_i1 GO:0003865,GO:0005575,GO:0005783 +TR2844|c0_g1_i1 GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234 +TR1837|c2_g1_i1 GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005737,GO:0006801,GO:0006810,GO:0006811,GO:0006812,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169,GO:0044237,GO:0044424,GO:0044464,GO:0044699,GO:0044710,GO:0044765,GO:0046872,GO:0046914,GO:0051234,GO:0055114,GO:0072593 +TR1678|c0_g1_i1 GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175 +TR3249|c0_g1_i1 GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175 +TR1479|c0_g1_i1 GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005737,GO:0006801,GO:0006810,GO:0006811,GO:0006812,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169,GO:0044237,GO:0044424,GO:0044464,GO:0044699,GO:0044710,GO:0044765,GO:0046872,GO:0046914,GO:0051234,GO:0055114,GO:0072593
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered/Trinity_filtered_exp.fasta Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,34 @@ +>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG +CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC +AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT +ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG +GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG +AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG +TATATGGTACAGATGTAAAG +>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT +TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT +ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA +TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC +>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT +TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA +TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT +TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT +AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT +ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA +AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC +CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG +GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT +G +>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC +AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC +CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC +ATACATGATTCTATTCAACCAA +>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG +CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT +ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA +TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered/Trinity_filtered_pct_iso.fasta Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,45 @@ +>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG +CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC +AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT +ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG +GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG +AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG +TATATGGTACAGATGTAAAG +>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT +TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT +ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA +TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC +>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA +ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC +AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG +AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA +AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA +>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT +TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA +TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT +TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT +AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT +ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA +AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC +CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG +GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT +G +>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA +GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC +TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG +TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC +>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC +AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC +CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC +ATACATGATTCTATTCAACCAA +>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG +CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT +ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA +TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered/counts.matrix Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,8 @@ + wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TRINITY_DN1_c0_g1_i1 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00 +TRINITY_DN0_c0_g1_i1 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00 +TRINITY_DN2_c0_g1_i1 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 +TRINITY_DN2_c1_g1_i1 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00 +TRINITY_DN2_c2_g1_i1 11.00 4.00 4.00 8.00 5.00 7.00 3.00 4.00 8.00 +TRINITY_DN2_c3_g1_i1 368.00 422.00 425.00 172.00 216.00 210.00 234.00 254.00 212.00 +TRINITY_DN3_c0_g1_i1 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/norm/Trinity.fasta Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,46 @@ +>TRINITY_DN1_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT +TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT +ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA +TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC +>TRINITY_DN0_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] +CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG +CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC +AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT +ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG +GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG +AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG +TATATGGTACAGATGTAAAG +>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] +TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA +ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC +AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG +AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA +AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA +>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT +TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA +TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT +TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT +AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT +ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA +AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC +CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG +GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT +G +>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] +ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA +GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC +TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG +TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC +>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] +GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC +AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC +CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC +ATACATGATTCTATTCAACCAA +>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG +CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT +ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA +TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw/Trinity.fasta Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,46 @@ +>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] +CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG +CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC +AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT +ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG +GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG +AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG +TATATGGTACAGATGTAAAG +>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT +TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT +ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA +TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC +>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] +TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA +ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC +AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG +AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA +AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA +>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT +TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA +TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT +TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT +AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT +ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA +AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC +CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG +GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT +G +>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] +ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA +GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC +TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG +TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC +>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] +GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC +AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC +CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC +ATACATGATTCTATTCAACCAA +>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG +CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT +ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA +TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw/map.tsv Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,7 @@ +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.left.fq Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,400 @@ +@61DFRAAXX100204:1:100:10494:3070/1 +ACTGCATCCTGGAAAGAATCAATGGTGGCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTTT ++ +ACCCCCCCCCCCCCCCCCCCCCCCCCCCCCBC?CCCCCCCCC@@CACCCCCACCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:100:10497:13422/1 +GTAATTTCCGTACCTGCCACAGTGTGGGCTCACCCTGCTTAGAGGACAGGGAAGGACCCTAAAGGTAGGCTGATGC ++ +CCCCCCCCCCCCCCCCCCCCCCDCDCCCCCCCCCCCCCCCCCCCDDCCDDCDCBDCCDDDDBADDADDB@DBBBA@ +@61DFRAAXX100204:1:100:10546:4478/1 +CTGGGCTGCAGCTAAGTTCTCTGCATCCTCCTTCTTGCTTGTGGCTGGGAAGAAGACAATGTTGTCGATGGTCTGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC7CB@CA:>AB?C=C@@@@?A@?5:88: +@61DFRAAXX100204:1:100:10609:6818/1 +CACGTTTTCTAAGCAGTTTGTACCAGATCGTGCTAACTGCTCATTGTCTTGTTGTACACACCAGTAAAGCTGGGCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:100:10648:5988/1 +TGCTCATTGTCTTGTTGTACACACCAGTAAAGCTGGGCAAAAATATCATCCAAAAGTACATCGCTGAGAACTCCTA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCDCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:100:11486:13583/1 +CCCACCTGAAAACATTTTCTACATCCACTGTTATATGGAATGCTTGATAAGCTTTTCATTCTAACCATCAGAGCAC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBC +@61DFRAAXX100204:1:100:1176:14271/1 +TCTGAATAAGTCCTGCCACCAATGTTTTTCATAAGTGTGGCCATATGTTTTCATTATTTCAAACATTACTGTTAAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCDCDCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCDBBABDB +@61DFRAAXX100204:1:100:12152:16425/1 +CTCCGTTTTTTGAGAGTGCAACACATAGATACTGCTTGATAGCATTAATAAACATCTCATTTGTCCTGAAAACAGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:100:14680:13081/1 +GCCTGAGTGTGCAAAAATCTTCAGAGTAAGAATACCATAGTTGCTAAATATCTTTTACCATGAGCAATAATTTTTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC;CCCCCC +@61DFRAAXX100204:1:100:16086:14019/1 +TCTGGTGCAGCTAGATGGAATACTGAGAAAATGTTCTTCCATCCTGAACGAATATTTGCAGCCTGAGAATTAACCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCBCCDDCDCC +@61DFRAAXX100204:1:100:17458:1622/1 +GTGAAAGGTCATCTATTTTAATGGCTTGTCTTTAAAAACCCTAAGAGAGGGAGGATGTCACAGGGAGGGCTTGTCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCC5A############################################### +@61DFRAAXX100204:1:100:17716:21197/1 +CCAGGCTTCCCGGTGACTTTCGGATGTTAGAGTGAGGAAGTAGCTCAGCGCTTCCCTGCAGACGTTTAAAAGCCTC ++ +CCCCCCCCCCCCCBCCCCCCCCC@CCCCCC@BBCCCCCCCBDB>CCCCAC@BCBBCDDBD@?BCBA@6BBB>;A;: +@61DFRAAXX100204:1:100:19734:13092/1 +ATCATCTTGGAGACTTTTATCCACATCATGTGTTTGGGGCTCAAGATCCCCTTCATGCTCTTGGTTTATATGATCA ++ +;CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCDC +@61DFRAAXX100204:1:100:2082:1789/1 +ACGGGTGTGGTGCCAAGCATCCCTTGTTCTTGGAGGTATTGTATTCCTCTCTTTGGTTTCTTATTAAATAAATCAA ++ +CCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCADCCCDBCCCCCCCCCCDABBCCDCC@CBBBDDDD;@B?= +@61DFRAAXX100204:1:100:2172:8797/1 +GCCAAAACATAAGCAGTATCTGCACTAGCAAAAAGGGTTTGTCCTTGGTTGCACTCTAGGGATCTTGCAGCAAATT ++ +############################################################################ +@61DFRAAXX100204:1:100:2238:12815/1 +ACCATAGTTGCTAAATATCTTTTACCATGAGCAATAATTTTTTTCTCCCTTCCCCCACCCCCAATTATAAACATTT ++ +############################################################################ +@61DFRAAXX100204:1:100:2327:5980/1 +CTCCTAAATAATTTCCATCAGTGTGGGCCACCGTGATGAGTGTTTTTATTGTGTCGATATTCTTCTGTTTCATTTC ++ +CCCCCCCCCCCCCCCCCCCCCCCCC0BBBACCCBCCCCCC=CCCCCB@B@=DC@CCDDBCC-CC@CABBBB<CCCA +@61DFRAAXX100204:1:100:3665:17139/1 +ATACTTCTTTGGGTAATTTCCGTACCTGCCACAGTGTGGGCTCACCCTGCTTAGAGGACAGGGAAGGACCCTAAAG ++ +CCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCDCBCCCCCCCCCCCCCCCCCCCCCCCCBCBCDCCCBDBA>DC +@61DFRAAXX100204:1:100:6480:5393/1 +TGGAGACTTTTATCCACATCATGTGTTTGGGGCTCAAGATCCCCTTCATGCTCTTGGTTTATATGATCAACAGTCT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCBCCCCBDCBDDADBDC +@61DFRAAXX100204:1:100:8693:14085/1 +AGCTATTTCGTTATAAATGGCTGATAGATACTCTTCAGGGAGATCTTTACTGTCATTGATACCACGATTCATTTTA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:100:9306:14527/1 +GTAGAATGATGCGTGAGCTTTAAACCTGCTGTCACTGATCTTCAGAACTTTAGTGAGGAACAGTAACAGTAAGTTA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCBACDCCBCDCBCC +@61DFRAAXX100204:1:100:9656:2687/1 +CTTCTAGGCAAAGAGAGGCTACTTCAGTATCATCACAGTCTTGGAGACCCACACTGAATGCAGCCAGAAAAGGTGT ++ +BBBBBBBBBBBBBBBBBBBBB>>B>;=;=7>>?>>B>>;>BB>B################################ +@61DFRAAXX100204:1:101:11219:19264/1 +TTTGCTAACTTCTTCACTCACAGTAGAAACAGAAACCAGTGGTGCTTGCTGTCTGTTATCTGAAGATCTNGGTTGA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCABCCCCCCCCCCCCCC@CBCC;DB<>>A&>99>;@ +@61DFRAAXX100204:1:101:11349:8542/1 +GGGTAATTTCCGTACCTGCCACAGTGTGGGCTCACCCTGCTTAGAGGACAGGGAAGGACCCTAAAGGTANGCTGAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCAA;A'??@=@> +@61DFRAAXX100204:1:101:11674:10443/1 +CACCCACACCCTGTCTTCAGGTGCCACGCTCATGTCATCACTTGTGTACTCCTTGAAAGCCTGCGGTCTNTCAGAC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCACCCCCCCCCCACC&AAA?AC +@61DFRAAXX100204:1:101:1179:19106/1 +TTGGTTGAATAGAATCATGTATGTCTACAGATTTTTGTGATATTGCATCCAACGGCTTTTCACTCACAGNTGATGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@BCCCCCCCCCCCCCCCCCACCCCADCCBCA@'AA=@?? +@61DFRAAXX100204:1:101:12110:12654/1 +CTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATCCGGAAGAGAATGCGCAGCCCACACGCCAGGCNGCTTGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCBCCDCCBCCDCCDCBCDAD@ABBDDDAD@BABB.625'?A=:@0 +@61DFRAAXX100204:1:101:13165:4417/1 +CTGGATTATCAGTGCCAGACATCTGTGTACTGTAGCTGCCAATTCCTGATGATGATGTGGATTCTAAGGNGTTTAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCA?&75:;8C +@61DFRAAXX100204:1:101:13420:13159/1 +GGTGGATCCCCTCCTGTTGTCATCTTGACAGGCATCAGCCACAACAGATTCAGGGCACAGCAAGCCCTCNAAATGA ++ +CCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACAC&89848C +@61DFRAAXX100204:1:101:14810:10441/1 +CAGGAAAGAATCAATGGTGGCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTCTGNAATGCA ++ +CCCCCCCCCCCCCCCCCDCCCCCCCCCCBCBCCCBBCCCCCCCBCCCDCCCCCCCDCCDCCCDCC:A?A'AAAAAC +@61DFRAAXX100204:1:101:15025:8342/1 +GTGGGTAGGAAGCCTCTGCTGCAGGATCCTTTCACAGAGCAGAGCAATGTAAACACCAACAGAAAAACANCGGCTC ++ +CCCCCDCCCCC@CCCCCCCCCCCCCCCCCCCCCCCCCDCCCCBDBCCBCDCCCDCCDCBDACBBD=999%8====B +@61DFRAAXX100204:1:101:15551:15592/1 +CTCCCAAAACCATGCCAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATNTACATC ++ +CCCCCCCCCCCCCCCCCCCDCCCCCCCCCBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCA=7A'AAB?AC +@61DFRAAXX100204:1:101:16061:6897/1 +ATGGAATGCTTGATAAGCTTTTCATTCTAACCATCAGAGCACAGTTCACAGTATGAATACATTTCCAGTNAATCTA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCDCCCCCCCDCCCCDC=C@'ABAAAC +@61DFRAAXX100204:1:101:16516:11581/1 +GGCCCTAAAGGTAGGCTGATGCTGTGGGAACAGCCTTTCTGCTCAATATGAGCCCAACACGCGACAGAGNCCACTG ++ +74/8588857;-84;<<<<<-88;8488+8A<286A9AA##################################### +@61DFRAAXX100204:1:101:17825:1193/1 +ACGCTCATGTCATCACTTGTGTACTCCTTGAAAGCCTGCGGTCTATCAGACACATATTTTGCACAATGGNGAATAA ++ +BCCCCCCCCCCCCCCCDCCCCCCCCCCCC@CBCCCCCCC@CCCCCBCDCCCCCCCCCCCCCCCCCAABA&A>>??A +@61DFRAAXX100204:1:101:2920:3823/1 +TCCATCAGAGCACAGTTCACAGTATGAATACATTTCCAGTAAATCTAACCTCCCAAAACCATGCCAGGTNTGTTAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB'CCBC@C +@61DFRAAXX100204:1:101:4549:18278/1 +AGGTGGATCCCCTCCTGTTGTCATCTTGACAGGCATCAGCCACAACAGATTCAGGGCACAGCAAGCCCTNAAAATG ++ +AB?BA:?B<?>:>:7;=BB=??>A>>>:+>//000BBBB@B@BBBBABBBB>B@?ABBBBBB>@############ +@61DFRAAXX100204:1:101:5059:19347/1 +TTTGGACTTGCCTTTGAAGCCTGCTTTCCACAGAGCAGTCCTCTGTTCATTGTTGGAATTAAATGCTTTNGCAAAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCC&89:79C +@61DFRAAXX100204:1:101:5741:4886/1 +CCCACCCCCAATTATAAACATTTTATCCTTCAAAATACAGCTCTCCTGAGTTGTACTTCTCGCAGAAGCNCAGTCT ++ +CCCCCCBBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'B?BAAC +@61DFRAAXX100204:1:101:6207:10801/1 +GCCAAAACATAAGCAGTATCTGCACTAGCAAAAAGGGTTTGTCCTTGGTTGCACTCTAGGTATCTTGCANCAAATT ++ +DCCCCCCCDBCCCCCCCCCCCCCCCCCCCCCAC@CAA9AACCCCCCCC@CCCCCCCCCCB@CCCC########### +@61DFRAAXX100204:1:101:6228:11229/1 +CAGTGATTCAAGTTTCAGTCTGTGAAAGGTCATCTATTTTAATGGCTTTTCTTTAAAAGCCCTAAGAGANTGAGTA ++ +CBCCCCCCCCCCCCC@CCBBCC@CC@<BB@C@CC@CC?CBC?C<CCC?CCC?>>:<5?/:>A?:A########### +@61DFRAAXX100204:1:101:7284:17741/1 +CAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATCTACATCAAGCCCCGNCACCCA ++ +CCCCCCCCCCCCCCBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCC@'CCCCCC +@61DFRAAXX100204:1:101:7317:19738/1 +ATGAGAATCAATATTGTACAGAAAGTTGTACAGAATTTTTTTACATAGAAAACTTTACATCTGTACCATNTACATA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCACC'AAAAA@ +@61DFRAAXX100204:1:101:7386:20759/1 +CCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTCTGAAATGCAAGTTCTACTATGNTTTCAT ++ +CCCCCCCCCCCCCCCBBCCCCCCCCCCCBCCCCCCCDCCCCCCDCCBCCCCCCDCCBBCBCCCCCCBBC)ACBA@D +@61DFRAAXX100204:1:101:7661:3279/1 +TTGGGGCTCAAGATCCCCTTCATGCTCTTGGTTTATATGATCAACAGTCTGAGGTGGCAAATATCTAAGNTGAGGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCC'@????= +@61DFRAAXX100204:1:101:7989:14539/1 +CGTGCTCCAAGTGTGTTGCACTTGTAAAAGGTGCCTGAACATGGCTCACAGCTTCCATGAGTGCTTTAGNCGTCTT ++ +CCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCBDCCCCCCCCCABCCCCCBCCCCCCBCC=CBCCCCCCC'AA<A@C +@61DFRAAXX100204:1:101:8630:9416/1 +GAGGGAGACAGGCGAGTAGGTGGCGGTGGGGGCGAGGAGGCGTGGATGCTAGCCGCCGTCTCCGTTAGCNTCCGTC ++ +############################################################################ +@61DFRAAXX100204:1:101:9622:17436/1 +GCCAAAACATAAGCAGTATCTGCACTAGCAAAAAGGGTTTGTCCTTGGTTGCACTCTAGGTATCTTGCANCAAATT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCBBCCCBBBB'AAA=AC +@61DFRAAXX100204:1:102:10071:12692/1 +TGCGTGAGCTTTAAATTTAAAAGCCTCTGCTGGANTTCTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATCC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'CCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDBCCDCCDDAC +@61DFRAAXX100204:1:102:10556:11503/1 +TCCTGGGATTCCATTTGCTTGGATGTTTTCACTGNCACTACCATCTTCTACAGTTCCAGTGTTGCCTTCTGTACTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'BBBBBCCCCCCCCCCCCCCCCCBCBCDCDCCCDBDBCAABB +@61DFRAAXX100204:1:102:10558:14342/1 +ATGTTTTCTACCTTGGTGGATCCCCTCCTGTTGTNATCTTGACAGGCATCAGCCACAACAGATTCAGGGCACAGCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCC'CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBC +@61DFRAAXX100204:1:102:12109:19420/1 +TCTGTTATCTGAAGATCTTGGTTGAATAGAATCANGTATGTCTACAGATTTTTGTGATATTGCATCTTACCAACGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'>????DCCCCCCCCCCCCC@BACCCCCCBCDCCCDCDBDDB +@61DFRAAXX100204:1:102:12757:13134/1 +GGGATGTATTGAACCACTGCTCTCAGGACAGGAANAAACAATGCACAAGCAATTTTCTTCCTAAATAACAATTCAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC)BBBBBCCCCCCCCCCCCCCCCCC@BCCCCCCCCCCACCCCC +@61DFRAAXX100204:1:102:13549:15464/1 +GTCCATGTACATCCGGAAGAGAATGCGCAGCCCANACGCCAGGCTGCTTGTCTCCTGTTTTAGAAGATTGGGCTTG ++ +CCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCC'CCCCCCCCCCC?CCCDCCBCCCBDCDBDDBBCADA<AC@BB +@61DFRAAXX100204:1:102:13777:6235/1 +CGCAGGACTCACAAGGGTAAAGCAAATTAAGAACNCGTCTGTCTGCGGGTAGGAGAGGGGACGCAATCTGTCATAC ++ +############################################################################ +@61DFRAAXX100204:1:102:14960:18241/1 +GCCACGAATTTCCTAAATAATTTCCATCAGTGTGNGCCACCGTGATGAGTGTTTTTATTGTGTCGATATTCTTCTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC&CCCCCCCCCCCCCCDCCCCCB@BB@DCCCCDCBCCCCCCCC +@61DFRAAXX100204:1:102:15063:6971/1 +CAGAAAAGGTGTCCAAGCCAACTTAAACATCGGCNTCACGTGCTCCAAGTGTGTTGCACTTGTAAAAGGTGCCTGA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'8;9;9CCCCCCC@CBCCCCCCCCCCCCCCCCDCAACBBBBC +@61DFRAAXX100204:1:102:16420:15231/1 +GTTGTACTTCTCGCAGAAGCTCAGTCTTTACATCNATACTTCTTTGGGTAATTTCCGTACCTGCCACAGTGTGGGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCC'CCCBCCCCACCCCCCDCCCDCDDDCAB@BDBBDDCBCACCB +@61DFRAAXX100204:1:102:16908:12433/1 +CACTGATGAAATAATTCAAAAACTTTATTGACCTNTAACCTGATTAGATATGCCAGATGAGAATCAATATTGTACA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCC +@61DFRAAXX100204:1:102:17677:10400/1 +CGCACATCTTATCCCTTCTAGGCAAAGAGAGGCTNCTTCAGTATCATCACAGTCTTGGAGACCCACACTGAATGCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC',00.-;7;<4?@>:A########################## +@61DFRAAXX100204:1:102:17711:7491/1 +ACTCTGGACAATATCAAGTGGCTTTTCTTCATAGNCTCCATCATACAAGATATCATTTTTAGATAATGTTTCAGCT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCC'CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCDCCCCBCA +@61DFRAAXX100204:1:102:17798:2084/1 +CCTTGTTCTTGGAGGTTTTGTATTCCTCTCTTTGNTTTCTTATTAAATAAATCAATCCCTTGTTCTATTATTTCTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBB'BBBBBCCCCCCCCCCBBCCACCCCCCCCCCCCCCDCCCCCC +@61DFRAAXX100204:1:102:18807:10059/1 +CTGCACTGGAAATATCAGATCCGTTTTCAGGCTCNGTATCATCTTGGAGACTTTTATCCACATCATGTGTTTGGGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC&CBCCCCCCCCCC@CDCCCCCCCDCDCDC@ACDBADDBB;BA +@61DFRAAXX100204:1:102:19518:11565/1 +CCTGGGAAGAAGACAATGTTGTCGATGGTCTGGANGAGTTCCAGCTGCACAACACATTTAATCAACAGGGCAGCAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCC'BAB>BCCCBCCCCCCCDDACABCCBACCACDAD@DDBD<>C +@61DFRAAXX100204:1:102:2639:2051/1 +CTGCCTCAGAGAGTCTACTGCAAATATGGCTACANCTTCATTAGGATTACAACCAACCTTATTAAAATGATCTCCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCAA3A########################################## +@61DFRAAXX100204:1:102:3101:2926/1 +CTTCCCAGGCACTGACTCTGCTCTCGTCCATGTANATCCGGAAGAGAATGCGCAGCCCACACGCCAGGCTGCTTGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'BBBBBCCBCCCCCCCCCCCCCCCCCCC<CCCDDCAAB@B<B +@61DFRAAXX100204:1:102:5977:14503/1 +GGGGGTTCGGCCTCGCCAGAGGTGGGACGCCAAGNCAGAAGCGCGTGAGGAATTGTGGTTTTGAAGATATCCAGGG ++ +CCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCCC'CCCCCCCCCCDCACCBCBCC?CCBCCCCAACDCCCBCDCCA +@61DFRAAXX100204:1:102:6251:21399/1 +CCCAGCTATTTCGTTATAAATGGCTGATAGATACNCTTCAGGGAGATCTTTACTGTCATTGATACCACGATTCATT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'BBBBACCCCCCCCCCC@CCCDCCCCCDCDCCBCCBCDD@CC +@61DFRAAXX100204:1:102:7093:4246/1 +CGGGTCTTGTCAGCAGGGATGTTTTCTACCTTGGNGGATCCCCTCCTGTTGTCATCTTGACAGGCATCAGCCACAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC(CCCCCCCCCCB@CDCCDCCCCCCCDDDCBDDBDDBDCDABB +@61DFRAAXX100204:1:102:7907:21314/1 +AGACACATATTTTGCACAATGGCGAATAAGTCGGNTTGCTTCCATACTTGTGTCTGGGAAAGCTGCATTACATGCG ++ +>BBB>BB>BBB<B?>?>??<99:<9:A<??0000%*000089:;<74;?8BABBBBA>B################# +@61DFRAAXX100204:1:102:8037:6949/1 +TCTAGGTATCTTGCAGCAAATTTTTCCATTAATCNATCAATTTTCTGAGCTTCTCCTGGAAGCCGGAATCCTTCCA ++ +CCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCC(BBBBBCCCCCCCCCCCCCCCCCCCBCCCCCCDDDCCCCCCC +@61DFRAAXX100204:1:102:8724:1888/1 +CGGGTGTGGTGCCAAGCATCCCTTGTTCTTGGAGNTATTGTATTCCTCTCTTTGGTTTCTTATTAAATAAATCAAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBB@B&28;88DCCCCCCCCCCCCCCDCCCCCBCCDC@BCA>@BD@B +@61DFRAAXX100204:1:102:8903:16361/1 +CCTATAAGTTGTGCCAGCTCTAACTGACTGATGCNCTTCAGGATCTCATGCCACGAATTTCCTAAATAATTTCCAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC(CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:102:9691:18717/1 +ATAAGTTGTGCCAGCTCTAACTGACTGATGCACTNCAGGATCTCATGCCACGAATTTCCTAAATAATTTCCATCAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'BABBACCCCCCC;CCCCCBCCCCCCCCCCCCCCCCDCCCAC +@61DFRAAXX100204:1:103:10201:1449/1 +CTGAACACTAGAAAGGCATCCTTTTGTAAAATGTGGGAAAACTTAGCACCAGGTGAAGGTCCTGAAGAATTTCCAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCCCDCCCCCCCC?CCBCCCCCACC;CCCCCCC +@61DFRAAXX100204:1:103:11572:6697/1 +CAAAATTGAAACTAAACATTCTAACCCCTTTTTTCGCAGGCTCAATTCCTGAACATTACTCATACCGAGTTCTTGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC8CDCCCCDD +@61DFRAAXX100204:1:103:12517:20251/1 +GCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTCTGAAATGCAAGTTCTACTATGCTTTCAT ++ +CCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:13105:12342/1 +CTGGACTTCTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATCCGGAAGAGAATGCGCAGCCCACACGCCAGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCBCCCB@CCCCCB?BCCCCCCB@C@B; +@61DFRAAXX100204:1:103:13548:1359/1 +GGTGACTTTCGGATGTTAGAGTGAGGAAGAAGCTCAGCGCTTCCCTGCAGACGTTTAAAAGCCTCTGCTGGACTTC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCC+??AA?CCCCCCCCCCDCCDCBDCBCC@BBDDBDDDDBBABBACAAB +@61DFRAAXX100204:1:103:13762:1440/1 +CTCCCTTCCCCCACCCCCAATTATAAACATTTTATCCTCCAAAATACAGCTCTCCTGAGTTGTACTTCTCGCTGAA ++ +CCCCCCCCCCCCCBBBBBBCCCCCCCCCC?CCCCCCCCCCCCACCCCCCCCCCCCCCCCDCCDCCCCCCCACCBB@ +@61DFRAAXX100204:1:103:13776:4298/1 +TGATATTTGAAATACTATTCCAATTCGCAGGAAAAATCTTCTAAGAACAGCACGCAGTTCCGGAATCAAGTCAAAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDC@BCC +@61DFRAAXX100204:1:103:13798:6365/1 +GGTCACAGTCATAATTTACATAAATGTCCACCACACTCTGAGCATCTGCACAGATCCTTGTCAGTGTCTGAATAAC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCC +@61DFRAAXX100204:1:103:14748:1375/1 +CCAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATCTACATCAAGCCCCGCCACCC ++ +CCCCCCCCCCCCCCCBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@BCCCCCCCCCACCCDBD@@DDB +@61DFRAAXX100204:1:103:16156:9928/1 +CATGAGCAATAATTTTTTTCTCCCTTCCCCCACCCCCAATTATAAACATTTTATCCTTCAAAATACAGCTCTCCTG ++ +CCCCCCCCCCCCCCCCCCBBBBCCCCCCCCCC@B@BB@CCCCCCCCCACCCCCCCCCCCCAACCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:16292:7311/1 +CTGGTTCTTACATCTAATTTGCATCTATTGATGATACAAGACAACTCAAAGAGGATCGGGAACCACCCTCTCACCC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDBCDCDCCCCCCCCCCBDC +@61DFRAAXX100204:1:103:1757:15756/1 +GGCAAAAATATCATCCAAAAGTACATCGCTGAGAACTTCTAAATACTGGGTGAATACATCACATATTGCATAAAGG ++ +CCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:19512:1223/1 +CTGTTAAGCCCCTGGTTCTTACATCTAATTTGCATCTATTGATGATACAAGACAACTCAAAGAGGATCGGGAACCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCDCCDADBB@C@BB@ +@61DFRAAXX100204:1:103:2005:9846/1 +TGCTTCCCTGCAGACGTTTAAAAGCCTCTGCTGGACTTCTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCBCCCCABDBBCBBDDDC +@61DFRAAXX100204:1:103:2755:14644/1 +CTTACATCTAATTTGCATCTATTGATGATACAAGACAACTCAAAGAGGATCGGGAACCACCCTCTCACCCACACCC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC=C +@61DFRAAXX100204:1:103:3597:13520/1 +GTTGTTGTGATGTTAAAAAGCGGTACATTCCTTGGTCTTGAGTATCAACTCGAACATCGAAGTCTACTACATCTCT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCDCCCCCCCCCCCCCCCCCDCBCCCCDADDCDCDC +@61DFRAAXX100204:1:103:4062:11566/1 +GATGATACAAGACAACTCAAAGAGGATCGGGAACCACCCTCTCACCCACACCCTGTCTTCAGGTGCCACGCTCATG ++ +CCCCCCCCCCCCCBCCCCCCCCCCCCBCCCCC@CACCBCCCCCCCCCACCBCC=@BCBAC3;;-6AC@C@C?@:AB +@61DFRAAXX100204:1:103:5147:16732/1 +CATGGTTACAAGTTGTTGTCATCCATTCAGCTTTCTCTGTCTGCTGTTCTGGCAATTTCATGTTGTCAAAGATTCT ++ +CCCCCCCCCC;????CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:6646:12936/1 +GTGCAACACATAGATACTGCTTGATAGCATTAATAAACATCTCATTTGTCCTGAAAACAGGTCCTGCATTCTGCAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCDC +@61DFRAAXX100204:1:103:7220:15954/1 +GAGGAATTGTGGTTTTGAAGATATCCAGGGTGCAGTTACACGTTTTATCCCAGATTTCAAGAGTAAACTTTTCACC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCABCCCCCCCA +@61DFRAAXX100204:1:103:7253:3680/1 +CTTTACATCTGTACCATATACATATCCACCTGAAAACATTTTCTACATCCACTGTTATATGGAATGCTTGATAAGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:8055:11636/1 +TTCCTGATGATGATGTGGATTCTAAGGAGTTTAAACTTCCATATCTGTTTATAGTCTCTGGGTGTTTAACTTCACT ++ +CCCCCCCCCCCCCCCCCC<CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCBCDCCCABCCCDCC +@61DFRAAXX100204:1:103:8348:14452/1 +GTCAGAGCACAGTTCACAGTATGAATACATTTCCAGTAAATCTAACCTCCCAAAACCATGCCAGGTTTGTTATTTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDBCCDCCCDCCCBCB +@61DFRAAXX100204:1:104:12460:3347/1 +CTGATGCTGTGGGAACAGCCTTTCTGCTCAACATGAGCCCAACACGAGACAGAGGCCACTGGGTTACTAAAGGGAC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCC@CCDCDDCCCCBCCDCBB@BBAAB +@61DFRAAXX100204:1:104:12993:12947/1 +GGTGAATACATCACATATTGCATAAAGGACATGGTTACAAGTTGTTGTCATCCATTCAGCTTTCTCTGTCTGCTGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:104:13501:6860/1 +GTGATATTTGAAATACTATTCCAATTCGCAGGAAAAATCTTCTAAGAACAGCACGCAGTTCCGGAATCAAGTCAAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCBCCCCCCACCCDCBCC>A
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.right.fq Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,400 @@ +@61DFRAAXX100204:1:100:10494:3070/2 +CTCAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCATCTAGCTGC ++ +C<CCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCACCCCCACCC= +@61DFRAAXX100204:1:100:10497:13422/2 +GAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCACCC +@61DFRAAXX100204:1:100:10546:4478/2 +CTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@BCDCBCCCCCCCCCCCACCCCCCCCCBDC +@61DFRAAXX100204:1:100:10609:6818/2 +AGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGCCCTTTATGCAATATGTGATGTATTCACCCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?CBCC +@61DFRAAXX100204:1:100:10648:5988/2 +AGATGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCACCCBCCBACC +@61DFRAAXX100204:1:100:11486:13583/2 +CTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCBBBB@CCDCCCCDB@BDCCABCDDCBBCCCBC@ +@61DFRAAXX100204:1:100:1176:14271/2 +TGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCG ++ +CCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCDCCCCCCCCCC:BBBACCABC@CDDAB@DDCABDDABDBB +@61DFRAAXX100204:1:100:12152:16425/2 +CCTTTCTAGTGTTCAGGTCATTGTGTAAGCTGTCAATGAAACCACTGTCAGATGGACCACCAGATCCAAAGTCTCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCC= +@61DFRAAXX100204:1:100:14680:13081/2 +CACAGCATCAGCCTACCTTTAGGGTCCTTCCCTGTCCTCTAAGCAGGGTGAGCCCACACTGTGGCAGGGACGGGAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCDCCCCCCCCCBCCDCCB'299@'9@ +@61DFRAAXX100204:1:100:16086:14019/2 +AGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACGACCTTTTGAACATATAATGAAACGAAACAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCBCCCCCC +@61DFRAAXX100204:1:100:17458:1622/2 +AAAACATTTGGGTTGAACTTTTAGTCTTTGGGGGAGTGGTGGTCATTTTGAGGGCTTGCTGTGCCCTGAATCTGTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@CCCCCBCCCCCCCDCCCDDCBDCBB@BABA=BBDB@AB< +@61DFRAAXX100204:1:100:17716:21197/2 +GCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCAC?CCDBBCCBD@BCBBBB@B??BBA=@A?@ +@61DFRAAXX100204:1:100:19734:13092/2 +GGCTTTACTTACCGCAGTGACATCACAACACATAGAAATCCATGAAGGAACTGTGCTGCAAGCTGTGAGGACATGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCC?CC@CBCCCBCAACCC +@61DFRAAXX100204:1:100:2082:1789/2 +GGAGCAAGGATCAGTATGTGAACCCCAACTCTCAAACTACCCTTGGTCAGGAAAAACCCTCAGAGCAAGAGATACG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCBCBCCCBCDBBDACCDBCDCA@B## +@61DFRAAXX100204:1:100:2172:8797/2 +TATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAA ++ +############################################################################ +@61DFRAAXX100204:1:100:2238:12815/2 +CCCCTCCAGACCCTTTAGAAACCCAGAGGCCTCGGGCTCGCGTGTGGCTCATTTTCGCCAGAAAGGCGGTTCCCAC ++ +############################################################################ +@61DFRAAXX100204:1:100:2327:5980/2 +CAAGACTGTGATGATACTGAAGTAGCCTCTCTTTGCCTAGAAGGGATAAGATGTGCTATCAGGATTGCATGCATTT ++ +CCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCACCCC?BCCCCACBCCBCCCCCCCDDDAA@CCDBBC +@61DFRAAXX100204:1:100:3665:17139/2 +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?CCCCCC@CC@@CB@@@@DABBBCBBB +@61DFRAAXX100204:1:100:6480:5393/2 +TGCTACAATATCTATTTAGCCAGCAAAAATCTCATCAATCAGACAACAGCCAAAGCTACTCTTACTGAAATGCTGA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB +@61DFRAAXX100204:1:100:8693:14085/2 +TGCAACCAAGGACAAACCCTTTTTGCTAGTGCAGATACTGCTTATGTTTTGGCCTACTCAATTATCATGTTGACTA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:100:9306:14527/2 +GCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGCTACTTCCTCACTCTAACATCCG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCC +@61DFRAAXX100204:1:100:9656:2687/2 +TAGAAATGGAACAGATGGCCAAGACGGCTAAAGCACTCATGGAAGCTGTGAGCCATGTTCAGGCACCTTTTACAAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCD3DBBCCCDCBBCCDCBDC +@61DFRAAXX100204:1:101:11219:19264/2 +GTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@B@CBBCCCADDCCA@BC +@61DFRAAXX100204:1:101:11349:8542/2 +GTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?DDD@CDDDDDBCBBCDDDBDABB)BBBB +@61DFRAAXX100204:1:101:11674:10443/2 +CTCTGAGGCAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACG ++ +CCCCCCCCCCC@CCCCBC?CC@CBBCCC=C@CCCCAC:B@BBCC>@=@@@B>@BC@ACBB@>CBB=0;C@BBCC/? +@61DFRAAXX100204:1:101:1179:19106/2 +AAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCBCCBBCCCCACCCCACCCCCCCCCCCCCCCCBABDB>D@BDDD@ +@61DFRAAXX100204:1:101:12110:12654/2 +GCAAGCACCACTGGTTTCTGTTTCTACTGTGAGTGAAGAAGTTAGCAAAGTGAAATCCACAGCAAAATTCCCAGAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCBCDCCCCCBCCCCCDCCBCDCCBCAACCDCCAA>BBC=B<B?B +@61DFRAAXX100204:1:101:13165:4417/2 +GGACATTTATGTAAATTATGACTGTGACCTAAATGCAGCAAATATATTTGAAAGACTAGTAAATGACCTGTCGAAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCAC +@61DFRAAXX100204:1:101:13420:13159/2 +CCGGAAATCATCATCTTTCTGTGAAAATGTACAGAGATGCAGGTCTGTAATATAAAAATCTTAAACATATTGTTCC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCDCCCCCCCCC@@CCCCBCCCCCCDCDBC@ +@61DFRAAXX100204:1:101:14810:10441/2 +GGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCBCCCCCC +@61DFRAAXX100204:1:101:15025:8342/2 +GCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCDCCDCDCACCB +@61DFRAAXX100204:1:101:15551:15592/2 +GACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCCCCCCCCCDCC@ +@61DFRAAXX100204:1:101:16061:6897/2 +GGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCC +@61DFRAAXX100204:1:101:16516:11581/2 +GATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTA ++ +C@CCCCCC@CCCCBBCBBCCC=@8@CC:CCCBC?C@@CC@C@>@@CCC>C>@>A<A8@8=<??<<=:C5>BCCBCC +@61DFRAAXX100204:1:101:17825:1193/2 +AACGAAGCAGGTCTCCAACAATTCGAGATATGGTTGTACGGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCCCCCCCCCCCBCCCCCCACCCDC<ABBBA +@61DFRAAXX100204:1:101:2920:3823/2 +CAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCA ++ +CCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCBCCCCCCCCCCCDCCCCCCCACCCCCCC=C? +@61DFRAAXX100204:1:101:4549:18278/2 +GTCTGTAATATAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTA ++ +CCCCCCCCCACCCCC@@CCCBB?CCCCCCCCCCCCCCCCCCCCCCCCCCC@@@CC@=CC@@@C@@CCCCCCCCACC +@61DFRAAXX100204:1:101:5059:19347/2 +AAGAAGACAATGTTGTCGATGGTCTGGATGAGTTCCAGCTGCACAACACATTTAATCAACAGGGCAGCAAACAATT ++ +CCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCDCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCCBCDADCA?ACC +@61DFRAAXX100204:1:101:5741:4886/2 +GGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTT ++ +CCCCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCACCCCBCC:CCCCCDCDCDCBCBCBC@BCCC@?BBCBCCBD +@61DFRAAXX100204:1:101:6207:10801/2 +GGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT ++ +CCCCCACCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCBCCCCACCCCCCCCD@BCBB@BBCABC +@61DFRAAXX100204:1:101:6228:11229/2 +CTGTAATATAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTAAA ++ +CCBBCCCCCCCCC@@CCC>CCCBBC??>@BCCCCCBBCCCCC@CCCBC@@@CC@@CC@@@C@>CCCCCCCCCCC@C +@61DFRAAXX100204:1:101:7284:17741/2 +AAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTAAATACCCATAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBCCB@CCBBBCBBCCCCCCCCCBCCCCCCCCCCBA +@61DFRAAXX100204:1:101:7317:19738/2 +CATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCBCCCCCCAAC?BCCCCDCCCCCDC@ +@61DFRAAXX100204:1:101:7386:20759/2 +GATGTAGCCATATTTGCAGTAGACTCTCTGAGGCAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCD@CACBDDB@CABCCCB@BBABBAABB>>BAB>?AA>AB +@61DFRAAXX100204:1:101:7661:3279/2 +GCTGCAAGCTGTGAGGACATGCTACAATATCTATTTAGCCAGCAAAAATCTCATCAATCAGACAACAGCCAAAGCT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCD@CCC +@61DFRAAXX100204:1:101:7989:14539/2 +TGACTACAGACCTTCACAGTCCACAGGTTAAAAACAAAATGACAAAAGAACAGTACATTAAAATGAATCGTGGTAT ++ +CDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBBBCCCCCCCC?BBCCCCCCCCCC@CCCCCCC?BCCBC= +@61DFRAAXX100204:1:101:8630:9416/2 +GGCGCAGGCACCTCCACCGGCCCCGCCTTCTCTCCGCAAACGCTCCACGCACACAAAGGAGGCCCTTGAGCCTCAA ++ +############################################################################ +@61DFRAAXX100204:1:101:9622:17436/2 +ACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCACCBCCCBCCCCCCCC +@61DFRAAXX100204:1:102:10071:12692/2 +GCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACCGCTTTTTAACATCAC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCDCCCCCDCCCCDCCCCCBC +@61DFRAAXX100204:1:102:10556:11503/2 +CGGATCTGATATTTCCAGTGCAGAAAATGAACAGACAGAAGCTGATCAGGCAACTGCAGCTGAAACATTATCTAAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCDCCC +@61DFRAAXX100204:1:102:10558:14342/2 +AGAGATGCAGGTCTGTAATATAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBCCBBCCBBBCBBC +@61DFRAAXX100204:1:102:12109:19420/2 +AAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCBCCC@CCCCCCCC?CCBCCADCDCAB +@61DFRAAXX100204:1:102:12757:13134/2 +CAACGGAGCAGATTGCGTCTCACACAGAGGAACGAGAGGAAGTCTGTAACGCTCAGAGACTTGATGACAGTTCTTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCBCCCDCCCCCBCDCDCDDDDDBDCBBBDCBDBDD +@61DFRAAXX100204:1:102:13549:15464/2 +GCAAGAAGGAGGATGCAGAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCA ++ +CCCCCCCCCCCCCCCCCCBCDCCCCCCCCCBCCCCCCCCCCCCCBCCCACC@CCCCCCCBDCCC=CC?CC?CCACA +@61DFRAAXX100204:1:102:13777:6235/2 +GAAGGCCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACACGACCATGAGCCGC ++ +############################################################################ +@61DFRAAXX100204:1:102:14960:18241/2 +GCTGCATTCAGTGTGGGTCTCCAAGACTGTGATGATACTGAAGTAGCCTCTCTTTGCCTAGAAGGGATAAGATGTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCACCCCCCCCCDC +@61DFRAAXX100204:1:102:15063:6971/2 +GTATCTATCAGCCATTTATAACGAAATAGCTGGGAAAAAAATATCAATGAAAGAAACAAAAGAACTAACAATCCCT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBBCCCCCCCCCCCBBCC@BBCBBCCCCC?CCCAC +@61DFRAAXX100204:1:102:16420:15231/2 +CTACTACCCTCTCTTATGTGAAATTATGCAATTTGACTTGATTCCGGAACTGCGTGCTGTTCTTAGAAGATTTTTC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCC@CCCCCCCC>@CCCCCCCCCBC@DCBCCC +@61DFRAAXX100204:1:102:16908:12433/2 +TGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCDCCCCCBCCACCCCBCC +@61DFRAAXX100204:1:102:17677:10400/2 +CAATCCCTACAAAGTCAACTAAACAGAATGTAGCCAGTGAAAAGCAAAGACGACTTCTGTATAACTTAGAAATGGA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCBCCCCACDCC;@BBB@C +@61DFRAAXX100204:1:102:17711:7491/2 +TATAAACCAAGAGCATGAAGGGGATCTTGAGCCCCAAACACATGATGTGGATAAAAGTCTCCAAGATGATACAGAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCDCCCCCCCADC=DCCBCDA +@61DFRAAXX100204:1:102:17798:2084/2 +AGTGAAGTTAAACACCCAGAGACTATAAACAGATATGGAAGTTTAAACTCCTTAGAATCCACATCATCATCAGGAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCDC +@61DFRAAXX100204:1:102:18807:10059/2 +CTACAATATCTATTTAGCCAGCAAAAATCTCATCAATCAGACAACAGCCAAAGCTACTCTTACTCAAATGCTGAAC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCACC +@61DFRAAXX100204:1:102:19518:11565/2 +CTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCBCC@BCCCDBCCDABDDDDCDBCBDCBDDA +@61DFRAAXX100204:1:102:2639:2051/2 +CAGGAGTCTATTGGAGAAACCAGCTCTCAAAGTGTGGTAGTTGCTGTGGATAGAATATTCACCGGATCCACAAGGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCDCCACCDCCCCCACCBCB@<A88>>5?>@>@17>A1;5;:=; +@61DFRAAXX100204:1:102:3101:2926/2 +GAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACC ++ +CCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCACCCCCCCCCCCDBCC +@61DFRAAXX100204:1:102:5977:14503/2 +GAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCDCDCDCCCCCCDCDCCCCCDBCDCB +@61DFRAAXX100204:1:102:6251:21399/2 +GTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCDCCCCDCCCCDCACCBCBCCBDDCC@D<BCBDDBDAB +@61DFRAAXX100204:1:102:7093:4246/2 +GAAGATTTTTGCACACTCAGGCTATCTGAGACACCGGAAATCATCATCTTTCTGTGAAAATGTACAGAGATGCAGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCBCCBCB@ABBBADB@C= +@61DFRAAXX100204:1:102:7907:21314/2 +GACTCTCTGAGGCAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGACTTCT ++ +@@@9@####################################################################### +@61DFRAAXX100204:1:102:8037:6949/2 +CTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAA ++ +CCCCCCCCCCCDCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCDCCCCCCCCADCBCCABCAD@C@ +@61DFRAAXX100204:1:102:8724:1888/2 +TGAACTCCTTAGAATCCACATCATCATCAGGAATTGGCAGCTACAGTACACAGATGTCTGGCACTGATAATCCAGA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@=B?@99;>?BB==<@=@A?B=<<BBB>DB2(?=;@ +@61DFRAAXX100204:1:102:8903:16361/2 +GCATTTTCAGCATTCAGCTGGAAAGAGATGCATATGTCCAAGCACTAGCCAGATTTACCTTACTTACAGTGAGTTC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCBCBCC +@61DFRAAXX100204:1:102:9691:18717/2 +CTAGAAGGGATAAGATGTGCTATCAGGATTGCATGCATTTTCAGCATTCAGCTGGAAAGAGATGCATATGTCCAAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:10201:1449/2 +GAGACTATGAAGAAAAGCCACTTGATATTGTCCAGAGCATTGTAGAAGAAATGTTGAACATCATTGTTGGAGACAT ++ +CCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCBCCCCCCCDCBCCCCDCCCCCCCDCCCCDCA@BCBBB? +@61DFRAAXX100204:1:103:11572:6697/2 +AGCTCATTTGACCATAAGTGGATGGTTATTCAGACACTGACAAGGATCTGTGCAGATGCTCAGAGTGTGGTGGACA ++ +CCCCCCCCCCCCCCCCCCAC???AAACCCCCCCCCCCCCCCCCCCBCCCCCCCC@CABCCCCAACBC>CB<A?:BB +@61DFRAAXX100204:1:103:12517:20251/2 +CAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACGACCTTTTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCCCCDDCDCCCCCCCDCDDDBCD +@61DFRAAXX100204:1:103:13105:12342/2 +TCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCBCDD@BAAA +@61DFRAAXX100204:1:103:13548:1359/2 +GGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCBDCDCCCBDCCCBDDBCCDDCDCADDBDC@B +@61DFRAAXX100204:1:103:13762:1440/2 +GAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCBCCCCCCCCDCCCDDCBCCCCB@BCC> +@61DFRAAXX100204:1:103:13776:4298/2 +CCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCBCCCCCCCC +@61DFRAAXX100204:1:103:13798:6365/2 +GTTTATTAATGCTATCAAGCAGTATCTATGTGTTGCACTCTCAAAAAACGGAGTCTCATCTGTTCCAGAGGTTTTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCCCCCCDCCDDCDCCBDDC@ +@61DFRAAXX100204:1:103:14748:1375/2 +TAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTAAATACCCATA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@BCCB=CCBBBC@@CCCACCCACCCCBCCCDD>DC +@61DFRAAXX100204:1:103:16156:9928/2 +CTCATGTTGAGCAGAAAGGCTGTTCCCACAGCATCAGCCTACCTTTAGGGTCCTTCCCTGTCCTCTAAGCAGGGTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCDCCCDCCDCCA@ACBABB?B +@61DFRAAXX100204:1:103:16292:7311/2 +CACCATTGATTCTTTCCAGGATGCAGTGAAGTGTTTGTCTGAATTCACATGTAATGCAGCTTTCCCAGACACAAGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCC5CCCCDCCCCCBCCBCCCBDDDBDBBBBCD +@61DFRAAXX100204:1:103:1757:15756/2 +TGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:19512:1223/2 +TGTCACTCTTGTATTTGAAAAACACTTTCCGGCCACCATTGATTCTTTCCAGGATGCAGTGAAGTGTTTGTCTGAA ++ +CCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCC@CBA8=A=CCACCCBCCA# +@61DFRAAXX100204:1:103:2005:9846/2 +TTTAATTCCAACAATGAACAGAGGGCTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA ++ +CCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBDDBCDCCDBDCBCCDDDCDADBBDDC +@61DFRAAXX100204:1:103:2755:14644/2 +GCTGCATCAGACCAAGATGAAAGCATAGTAGAACTTGCATTTCAGACAACAGGGCACATTGTCACTCTTGTATTTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCACCCCC>CCC@CBACDCCDCC +@61DFRAAXX100204:1:103:3597:13520/2 +CACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCACACDDCCDDCCB@A?B@BB@ABBBBADABD<?>AA +@61DFRAAXX100204:1:103:4062:11566/2 +CAACAATTCGAGATATGGTTGTACGGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATG ++ +CCCCCCCBCCCCCCCCCCCCC?CCCC=CCCCCA=@A@CCACBCC?ABAABCCCCACC>BC<CCCACCCCB@C@B@? +@61DFRAAXX100204:1:103:5147:16732/2 +GGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCBCCCBCCCCCCCBCCBBCCBC +@61DFRAAXX100204:1:103:6646:12936/2 +CTCCAATGATACTCAGGAATCTGGAAATTCTTCAGGACCTTCACCTGGTGCTAAGTTTTCCCACATTTTACAAAAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCC@CDCCDCCCCCDCCCDBDBADDC +@61DFRAAXX100204:1:103:7220:15954/2 +GATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBCCCCCCCCCCCCCBCDC +@61DFRAAXX100204:1:103:7253:3680/2 +GTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTT ++ +CCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@BCCCCCCCBCDCCCBCCCCCCB=CDA +@61DFRAAXX100204:1:103:8055:11636/2 +AAATGACCTGTCGAAAATTGCACAAGGAAGGGGCAGCCAAGAACTTGGTATGAGTAATGTTCAGGAATTGAGCCTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCDCCCCDACCCCCCCCCACCCCC +@61DFRAAXX100204:1:103:8348:14452/2 +AACATTTGGGTTGAACTTTTAGTCTTTGGGGGAGTGGTGGTCATTTTGAGGGCTTGCTGTGCCCTGAATCTGTTGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@CCCCCDCCCCCCCCCCCCCACBCCDCCCCCAB@CBCCDCBB +@61DFRAAXX100204:1:104:12460:3347/2 +CACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTTACATTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCBCCC@@@BBCCCACBCCC@ACBC +@61DFRAAXX100204:1:104:12993:12947/2 +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTTGCCATTGTGCAAAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCC@CCACBCDDCBCC,BBC?BBBBB@BBBD +@61DFRAAXX100204:1:104:13501:6860/2 +CTGAGCTACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samples.tsv Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,4 @@ +ConditionA CondA_replicate1 +ConditionA CondA_replicate2 +ConditionB CondB_replicate1 +ConditionB CondB_replicate2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Nov 21 11:59:35 2016 -0500 @@ -0,0 +1,30 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="trinity" version="2.2.0"> + <repository changeset_revision="76d63b5c571a" name="package_trinity_2_2_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bowtie" version="1.1.2"> + <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bowtie2" version="2.2.6"> + <repository changeset_revision="0d9cd7487cc9" name="package_bowtie_2_2_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bioconductor-edger" version="3.14.0"> + <repository changeset_revision="5f4abad5b2c1" name="package_bioconductor_edger_3_14_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="rsem" version="1.2.28"> + <repository changeset_revision="4567331d510a" name="package_rsem_1_2_28" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="eXpress" version="1.5.1"> + <repository changeset_revision="93017e8743e5" name="package_express_1_5_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bioconductor-limma" version="3.28.10"> + <repository changeset_revision="b313488c66bd" name="package_bioconductor_limma_3_28_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="deseq2" version="1.10.0"> + <repository changeset_revision="e4a11a7d33d6" name="package_deseq2_1_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <set_environment version="1.0"> + <environment_variable action="set_to" name="TRINITY_MEM_OPTIONS">'--max_memory 30G --bflyHeapSpaceMax 30G'</environment_variable> + </set_environment> +</tool_dependency>