Mercurial > repos > iuc > qualimap_rnaseq
changeset 0:613e6446ea5d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qualimap_macros.xml Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,40 @@ +<macros> + <token name="@VERSION@">2.2.2c</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">qualimap</requirement> + <yield /> + </requirements> + </xml> + + <xml name="version_command"> + <version_command>qualimap --help | grep 'QualiMap v.' | cut -d '.' -f 2-</version_command> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btv566</citation> + <citation type="doi">10.1093/bioinformatics/bts503</citation> + <yield /> + </citations> + </xml> + + <token name="@SET_JAVA_OPTS@"> + export JAVA_OPTS="-Djava.awt.headless=true -Xmx\${GALAXY_MEMORY_MB:-1024}m" + </token> + + <token name="@MASSAGE_OUTPUT@"><![CDATA[ + sed 's|images_${report_name}/||g;s|css/||g' results/${report_name}.html > '$output_html' && + mkdir '${output_html.extra_files_path}' && + mv results/css/*.css '${output_html.extra_files_path}' && + mv results/css/*.png '${output_html.extra_files_path}' && + if [ -d results/images_${report_name} ]; then + mv results/images_${report_name}/* '${output_html.extra_files_path}' && + for file in \$(ls -A results/raw_data_${report_name}); do mv "results/raw_data_${report_name}/\$file" `echo "results/\$file" | sed 's/(//;s/)//'`; done + fi + #if $summary_report: + && mv results/$summary_report results/summary_report.txt + #end if + ]]></token> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qualimap_rnaseq.xml Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,383 @@ +<tool id="qualimap_rnaseq" name="QualiMap RNA-Seq QC" version="@VERSION@"> + <macros> + <import>qualimap_macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ + @SET_JAVA_OPTS@ && + + qualimap rnaseq + -bam '${seq_info.input}' + -gtf '$features' + ${seq_info.treat_as_pe} + ${seq_info.sorted} + ${counts_out.report_counts} + --sequencing-protocol ${read_filtering.library_type} + --algorithm ${read_filtering.treat_multimappers} + -outdir results -outformat html && + + #set $report_name = 'qualimapReport' + #set $summary_report = 'rnaseq_qc_results.txt' + #if str($counts_out.report_counts): + #set $ccol_name = str($counts_out.ccol_name).strip() or str($seq_info.input.name).replace(' ', '_') + printf '#GeneID\t%s\n' '$ccol_name' > '$output_counts' && + cat results/counts.txt >> '$output_counts' && + #end if + @MASSAGE_OUTPUT@ + ]]></command> + <inputs> + <conditional name="seq_info"> + <param argument="-pe" name="treat_as_pe" type="select" + label="Counting mode" + help="You will usually want to choose 'Count fragments' for paired-end data. For single-end data, choose 'Count reads'. See tool help below."> + <option value="">Count reads</option> + <option value="--paired">Count fragments</option> + </param> + <when value=""> + <param argument="-bam" name="input" type="data" format="bam" + label="Mapped reads input dataset" /> + <param name="sorted" type="hidden" value="" /> + </when> + <when value="--paired"> + <param argument="-bam" name="input" type="data" format="qname_sorted.bam" + label="Mapped reads input dataset" /> + <param name="sorted" type="hidden" value="--sorted" /> + </when> + </conditional> + <param argument="-gtf" name="features" type="data" format="gtf" + label="Genome annotation data" /> + <conditional name="counts_out"> + <param argument="-oc" name="report_counts" type="select" + label="Keep the per-gene counts data?" + help="The resulting dataset can, for example, serve as input to QualiMap Counts QC for further assessment."> + <option value="">No, just report statistics</option> + <option value="-oc counts.txt">Yes, generate separate counts output</option> + </param> + <when value="" /> + <when value="-oc counts.txt"> + <param name="ccol_name" type="text" + label="Name to use for the counts column" + help="Consider using the name of the analyzed sample here. Default: Name of the mapped reads input dataset in the history" /> + </when> + </conditional> + <section name="read_filtering" title="Read selection for counting" expanded="true"> + <param argument="-p" name="library_type" type="select" display="radio" + label="Strandedness"> + <option value="non-strand-specific">Count reads/fragments independent of strandedness</option> + <option value="strand-specific-forward">Count only reads/fragments expected in forward-stranded data</option> + <option value="strand-specific-reverse">Count only reads/fragments expected in reverse-stranded data</option> + </param> + <param argument="-a" name="treat_multimappers" type="select" display="radio" + label="Multimapping reads"> + <option value="uniquely-mapped-reads">Count uniquely mapped reads only</option> + <option value="proportional">Count also multimapping reads</option> + </param> + </section> + </inputs> + <outputs> + <data name="output_html" format="html" + label="${tool.name} report on ${on_string}" /> + <data name="output_counts" format="tsv" + label="${tool.name} counts on ${on_string}"> + <filter>str(counts_out['report_counts'])</filter> + </data> + <collection name="raw_data" type="list" + label="Raw data for ${tool.name} on ${on_string}"> + <data name="rnaseq_qc_results" format="txt" from_work_dir="results/summary_report.txt" /> + <data name="coverage_profile_along_genes_high" format="tsv" from_work_dir="results/coverage_profile_along_genes_high.txt" /> + <data name="coverage_profile_along_genes_low" format="tsv" from_work_dir="results/coverage_profile_along_genes_low.txt" /> + <data name="coverage_profile_along_genes_total" format="tsv" from_work_dir="results/coverage_profile_along_genes_total.txt" /> + </collection> + </outputs> + <tests> + <test expect_num_outputs="6"> + <conditional name="seq_info"> + <param name="treat_as_pe" value="" /> + <param name="input" value="test_mapped_reads.bam" /> + </conditional> + <param name="features" value="features.gtf" /> + <output name="output_html" ftype="html"> + <assert_contents> + <has_text text="Qualimap report: RNA Seq QC" /> + </assert_contents> + </output> + <output_collection name="raw_data" type="list"> + <element name="rnaseq_qc_results" file="rnaseq_qc_results_default.txt" ftype="txt" compare="diff" lines_diff="4" /> + </output_collection> + </test> + <test expect_num_outputs="7"> + <conditional name="seq_info"> + <param name="treat_as_pe" value="--paired" /> + <param name="input" value="test_mapped_reads.bam" /> + </conditional> + <param name="features" value="features.gtf" /> + <conditional name="counts_out"> + <param name="report_counts" value="-oc counts.txt" /> + <param name="ccol_name" value="try_this" /> + </conditional> + <section name="read_filtering"> + <param name="library_type" value="strand-specific-forward" /> + <param name="treat_multimappers" value="proportional" /> + </section> + <output name="output_html" ftype="html"> + <assert_contents> + <has_text text="Qualimap report: RNA Seq QC" /> + </assert_contents> + </output> + <output name="output_counts" file="rnaseq_qc_counts_custom.txt" ftype="tsv" /> + <output_collection name="raw_data" type="list"> + <element name="rnaseq_qc_results" file="rnaseq_qc_results_custom.txt" ftype="txt" compare="diff" lines_diff="4" /> + </output_collection> + </test> + </tests> + <help><![CDATA[ +**What it does** + +**Qualimap RNA-Seq QC** reports quality control metrics and bias estimations +which are specific for whole transcriptome sequencing, including reads genomic +origin, junction analysis, transcript coverage and 5’-3’ bias computation. +As such, the tool complements the more general analysis with QualiMap BamQC, +and its (optional) gene counts output can be analyzed further with QualiMap +Counts QC. + + +Input +===== + +*Mapped reads input dataset* + +The dataset holding the mapped reads to carry out the analysis with. Typically, +this will have been produced by a splicing-aware aligner like *HISAT2* or *RNA +STAR*. + +*Genome annotation data* + +A GTF dataset of genomic features that mapped reads should be counted for. + + +Parameters +---------- + +*Counting mode* + +Determines whether reads should be counted individually, or whether multiple +reads originating from the same sequencing template (*i.e.*, the read and its +mate in paired-end sequencing) should be counted as one. + +You will usually want to choose ``Count fragments`` for paired-end data. For +single-end data, choose ``Count reads``. + +*Keep the per-gene counts data?* + +Controls whether the optional Counts output dataset should be produced, or not. + +If you choose to produce this dataset, you can use: + +*Name to use for the counts column* to specify the name of the second column in +that output. + +Using, for example, the name of the analyzed sample here can help you keep +track of your data, especially when joining several counts datasets into a +count matrix later on. In addition, *Qualimap Counts QC* will reuse the +names of counts columns as sample names. + +**Read selection for counting** section + +*Strandedness* + +Choose here the option that fits the strand-specificity of your sequencing +library. + +The Galaxy Training Material has an excellent discussion of sequencing +data strandedness included in the +`Reference-based RNA-Seq data analysis <https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html#count-the-number-of-reads-per-annotated-gene>`__ +tutorial. + +*Multimapping reads* + +Choose here how to treat reads that are mapped ambiguously to several genome locations. + +- *Count uniquely mapped reads only* excludes multi-mapping reads + +- *Count also multimapping reads* activates *proportional* counting of + multi-mapping reads. + + In this mode, each read is weighted according to the number of mapped + locations. For example, a read mapped to 4 different locations will add 0.25 + to the "counts" of each of the locations it maps to. The final calculated + counts per feature will be converted to integer numbers. + +Note: Detection of multi-mapping reads by the tool relies on the ``NH`` tag of +reads in the BAM input, so make sure the aligner used to produce the dataset is +configured to write this tag. + + +Outputs +======= + +HTML Report +----------- + +**Summary Section** + +*Reads alignment* + +Summarizes the mapping characteristics of the reads in the input: + +- total number of mapped reads + + reported as left/right read mates in case of paired-end reads; excludes + secondary alignments + + If you accidentally selected `Count fragments` as the *Counting mode* for + single-end data these and the following count of *Number of aligned pairs* + will be zero. + +- total number of alignments + + reports all alignment records found, including secondary alignments + +- number of secondary alignments + +- number of non-unique alignments + + reports the number of alignment records with an ``NH`` tag greater than one; + corresponds to the number of alignments that will have been skipped during + counting when *Count uniquely mapped reads only* is selected + +- number of reads aligned to genes + +- number of ambiguous alignments + + This is the number of mapped reads that span multiple annotated genes. + Such reads are always skipped during counting. + +- no feature assigned + + reports the number of alignments that are not overlapping any annotated + feature; these may represent alignments to introns or intergenic regions, or, + if the number is really high, may indicate a problem with your genome + annotations + +- not aligned + + number of reads not mapped by the aligner (but included in the BAM input) + +- strand specificity estimation (fwd/rev) + + computed if *Count reads/fragments independent of strandedness* is selected; + estimate of the proportion of alignments in line with forward- and reverse- + strand-specificitiy of the sequencing library + + Balanced proportions (*i.e.* ~ 0.5 forward- and ~ 0.5 reverse-strand support) + can be interpreted as likely non-strand-specificity of the sequencing library, + while a strand-specific library would manifest itself in a large fraction of + reads supporting that specific strand-specificity. + +*Reads genomic origin* + +Lists how many alignments (absolute number/fraction) fall into + +- exonic, +- intronic, +- intergenic + +regions, or are at least + +- overlapping an exon. + +*Transcript coverage profile* + +The profile provides ratios between mean coverage of 5’ regions, 3’ regions and whole transcripts. + +- 5’ bias + + the ratio of coverage median of 5’ regions (defined as the first 100 nts) to whole transcripts + +- 3' bias + + the ratio of coverage median of 3’ regions (defined as the last 100 nts) to whole transcripts + +- 5’-3’ bias + + the ratio of 5' bias to 3' bias. + +*Junction analysis* + +Lists the total number of reads with splice junctions and the relative +frequency of the (up to) 10 most frequent junction sequences. + + +**Plots** + +*Reads Genomic Origin* + +A pie chart showing how many read alignments fall into exonic, intronic and +intergenic regions. + +*Coverage Profile Along Genes (Total)* + +This plot shows the mean coverage profile of all genes with non-zero +overall coverage. + +*Coverage Profile Along Genes (Low)* + +The plot shows the mean coverage profile of the 500 genes with the lowest, but non-zero overall coverage. + +*Coverage Profile Along Genes (High)* + +The plot shows the mean coverage profile of the 500 genes with the highest +overall coverage. + +*Coverage Histogram (0-50x)* + +Coverage of genes from 0 to 50x. Genes with >50x coverage are added to the 50x +bin. + +*Junction Analysis* + +This pie chart shows an analysis of the splice junctions observed in the +alignments. It consists of three categories: + +- Known + + observed splice junctions both sides of which are in line with the genome + annotation data + +- Partly known + + observed splice junctions for which only one junction side can be deduced + from the genome annotation data + +- Novel + + observed splice junctions not predicted on either side by the genome + annotation data + + +Raw data +-------- + +This is a *Collection* of 4 individual datasets. + +Of these, the *rnaseq_qc_results* dataset provides a plain-text version of the +*HTML report* *Summary* section. + +The other 3 datasets hold the tabular raw data underlying the three coverage +profile plots in the *HTML Report*. + + +Counts data +----------- + +Optional. This is a 2-column tabular dataset of read or fragment counts +(depending on the chosen *Counting mode*) per annotated gene. The first column +lists the gene identifiers found in the *Genome annotation data*, the second +the associated counts. + +This dataset represents valid (single-sample) input for the QualiMap Counts QC +tool. + ]]></help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coverage_across_reference.txt Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,326 @@ +#Position (bp) Coverage Std +1.5 0.0 0.0 +3.5 0.0 0.0 +5.5 0.0 0.0 +7.5 0.0 0.0 +9.5 0.0 0.0 +11.5 0.0 0.0 +13.5 0.0 0.0 +15.5 0.0 0.0 +17.5 0.0 0.0 +19.5 0.0 0.0 +21.5 0.0 0.0 +23.5 0.0 0.0 +25.5 0.0 0.0 +27.5 0.0 0.0 +29.5 0.0 0.0 +31.5 0.0 0.0 +33.5 0.0 0.0 +35.5 0.0 0.0 +37.5 0.0 0.0 +39.5 0.0 0.0 +41.5 0.0 0.0 +43.5 0.0 0.0 +45.5 0.0 0.0 +47.5 0.0 0.0 +49.5 0.0 0.0 +51.5 0.0 0.0 +53.5 1.0 0.0 +55.5 2.5 1.5811388300841898 +57.5 3.5 1.8708286933869707 +59.5 4.0 0.0 +61.5 5.0 0.0 +63.5 5.0 0.0 +65.5 5.0 0.0 +67.5 5.0 0.0 +69.5 5.0 0.0 +71.5 5.5 2.345207879911715 +73.5 6.0 0.0 +75.5 6.0 0.0 +77.5 7.0 1.0 +79.5 8.0 0.0 +81.5 8.0 0.0 +83.5 9.0 0.0 +85.5 9.5 3.082207001484488 +87.5 10.5 3.24037034920393 +89.5 12.0 0.0 +91.5 13.5 3.6742346141747673 +93.5 15.0 1.0 +95.5 16.5 4.06201920231798 +97.5 17.5 4.183300132670378 +99.5 18.0 0.0 +101.5 21.5 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0.0 +569.5 0.0 0.0 +571.5 0.0 0.0 +573.5 0.0 0.0 +575.5 0.0 0.0 +577.5 0.0 0.0 +579.5 0.0 0.0 +581.5 0.0 0.0 +583.5 0.0 0.0 +585.5 0.0 0.0 +587.5 0.0 0.0 +589.5 0.0 0.0 +591.5 0.0 0.0 +593.5 0.0 0.0 +595.5 0.0 0.0 +597.5 0.0 0.0 +599.5 0.0 0.0 +601.5 0.0 0.0 +603.5 0.0 0.0 +605.5 0.0 0.0 +607.5 0.0 0.0 +609.5 0.0 0.0 +611.5 0.0 0.0 +613.5 0.0 0.0 +615.5 0.0 0.0 +617.5 0.0 0.0 +619.5 0.0 0.0 +621.5 0.0 0.0 +623.5 0.0 0.0 +625.5 0.0 0.0 +627.5 0.0 0.0 +629.5 0.0 0.0 +631.5 0.0 0.0 +633.5 0.0 0.0 +635.5 0.0 0.0 +637.5 0.0 0.0 +639.5 0.0 0.0 +641.5 0.0 0.0 +643.5 0.0 0.0 +645.5 0.0 0.0 +647.5 0.0 0.0 +649.5 0.0 0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coverage_histogram.txt Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,36 @@ +#Coverage Number of genomic locations +0.0 102.0 +1.0 2.0 +2.0 1.0 +3.0 2.0 +4.0 3.0 +5.0 11.0 +6.0 6.0 +8.0 5.0 +9.0 3.0 +10.0 2.0 +11.0 1.0 +12.0 2.0 +13.0 1.0 +14.0 2.0 +16.0 2.0 +17.0 2.0 +18.0 3.0 +21.0 1.0 +22.0 1.0 +23.0 3.0 +24.0 1.0 +25.0 8.0 +26.0 7.0 +27.0 3.0 +28.0 8.0 +29.0 11.0 +30.0 10.0 +31.0 20.0 +32.0 27.0 +33.0 11.0 +34.0 5.0 +35.0 4.0 +36.0 13.0 +37.0 8.0 +38.0 9.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/duplication_rate_histogram.txt Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,51 @@ +#Duplication rate Coverage +1.0 57.0 +2.0 8.0 +3.0 3.0 +4.0 0.0 +5.0 0.0 +6.0 0.0 +7.0 0.0 +8.0 0.0 +9.0 0.0 +10.0 0.0 +11.0 0.0 +12.0 0.0 +13.0 0.0 +14.0 0.0 +15.0 0.0 +16.0 0.0 +17.0 0.0 +18.0 0.0 +19.0 0.0 +20.0 0.0 +21.0 0.0 +22.0 0.0 +23.0 0.0 +24.0 0.0 +25.0 0.0 +26.0 0.0 +27.0 0.0 +28.0 0.0 +29.0 0.0 +30.0 0.0 +31.0 0.0 +32.0 0.0 +33.0 0.0 +34.0 0.0 +35.0 0.0 +36.0 0.0 +37.0 0.0 +38.0 0.0 +39.0 0.0 +40.0 0.0 +41.0 0.0 +42.0 0.0 +43.0 0.0 +44.0 0.0 +45.0 0.0 +46.0 0.0 +47.0 0.0 +48.0 0.0 +49.0 0.0 +50.0 0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features.gtf Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,4 @@ +test_chromosome test gene 1 300 . + . gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1"; +test_chromosome test transcript 1 300 . + . gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1"; +test_chromosome test exon 1 300 . + . gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1"; +test_chromosome test CDS 100 250 . + . gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_fraction_coverage.txt Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,52 @@ +#Coverage (X) Coverage +1.0 66.0 +2.0 65.33333333333334 +3.0 65.0 +4.0 64.33333333333334 +5.0 63.333333333333336 +6.0 59.66666666666667 +7.0 57.66666666666667 +8.0 57.66666666666667 +9.0 56.00000000000001 +10.0 55.00000000000001 +11.0 54.33333333333334 +12.0 54.00000000000001 +13.0 53.33333333333334 +14.0 53.00000000000001 +15.0 52.33333333333334 +16.0 52.33333333333334 +17.0 51.66666666666668 +18.0 51.000000000000014 +19.0 50.000000000000014 +20.0 50.000000000000014 +21.0 50.000000000000014 +22.0 49.66666666666668 +23.0 49.33333333333334 +24.0 48.33333333333334 +25.0 48.00000000000001 +26.0 45.33333333333334 +27.0 43.00000000000001 +28.0 42.00000000000001 +29.0 39.33333333333334 +30.0 35.66666666666667 +31.0 32.33333333333334 +32.0 25.66666666666667 +33.0 16.66666666666667 +34.0 13.0 +35.0 11.333333333333329 +36.0 10.0 +37.0 5.666666666666671 +38.0 3.0 +39.0 0.0 +40.0 0.0 +41.0 0.0 +42.0 0.0 +43.0 0.0 +44.0 0.0 +45.0 0.0 +46.0 0.0 +47.0 0.0 +48.0 0.0 +49.0 0.0 +50.0 0.0 +51.0 0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results_default.txt Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,122 @@ +BamQC report +----------------------------------- + +>>>>>>> Input + + bam file = /tmp/tmprT4oZK/files/b/1/f/dataset_b1fbaad4-1b5a-4769-8a15-b4cec4de5731.dat + outfile = results/genome_results.txt + + +>>>>>>> Reference + + number of bases = 650 bp + number of contigs = 1 + + +>>>>>>> Globals + + number of windows = 325 + + number of reads = 100 + number of mapped reads = 100 (100%) + number of secondary alignments = 1 + + number of mapped bases = 12,665 bp + number of sequenced bases = 7,465 bp + number of aligned bases = 0 bp + number of duplicated reads (estimated) = 18 + duplication rate = 15.85% + + +>>>>>>> Insert size + + mean insert size = 0 + std insert size = 0 + median insert size = 0 + + +>>>>>>> Mapping quality + + mean mapping quality = 115.8402 + + +>>>>>>> ACTG content + + number of A's = 1,910 bp (25.59%) + number of C's = 1,902 bp (25.48%) + number of T's = 1,497 bp (20.05%) + number of G's = 2,156 bp (28.88%) + number of N's = 0 bp (0%) + + GC percentage = 54.36% + + +>>>>>>> Mismatches and indels + + general error rate = 0.0118 + number of mismatches = 149 + + +>>>>>>> Coverage + + mean coverageData = 19.4846X + std coverageData = 16.5813X + + There is a 45.85% of reference with a coverageData >= 1X + There is a 45.38% of reference with a coverageData >= 2X + There is a 44.92% of reference with a coverageData >= 3X + There is a 44.62% of reference with a coverageData >= 4X + There is a 43.85% of reference with a coverageData >= 5X + There is a 41.85% of reference with a coverageData >= 6X + There is a 40.46% of reference with a coverageData >= 7X + There is a 39.85% of reference with a coverageData >= 8X + There is a 38.77% of reference with a coverageData >= 9X + There is a 38% of reference with a coverageData >= 10X + There is a 37.23% of reference with a coverageData >= 11X + There is a 36.92% of reference with a coverageData >= 12X + There is a 36.46% of reference with a coverageData >= 13X + There is a 36.15% of reference with a coverageData >= 14X + There is a 35.54% of reference with a coverageData >= 15X + There is a 35.23% of reference with a coverageData >= 16X + There is a 34.77% of reference with a coverageData >= 17X + There is a 34% of reference with a coverageData >= 18X + There is a 33.38% of reference with a coverageData >= 19X + There is a 33.38% of reference with a coverageData >= 20X + There is a 33.23% of reference with a coverageData >= 21X + There is a 31.85% of reference with a coverageData >= 22X + There is a 31.54% of reference with a coverageData >= 23X + There is a 30.92% of reference with a coverageData >= 24X + There is a 30.62% of reference with a coverageData >= 25X + There is a 28.62% of reference with a coverageData >= 26X + There is a 27.54% of reference with a coverageData >= 27X + There is a 26.92% of reference with a coverageData >= 28X + There is a 25.23% of reference with a coverageData >= 29X + There is a 23.38% of reference with a coverageData >= 30X + There is a 20.77% of reference with a coverageData >= 31X + There is a 16.77% of reference with a coverageData >= 32X + There is a 12.15% of reference with a coverageData >= 33X + There is a 10.15% of reference with a coverageData >= 34X + There is a 8.62% of reference with a coverageData >= 35X + There is a 7.38% of reference with a coverageData >= 36X + There is a 4% of reference with a coverageData >= 37X + There is a 1.85% of reference with a coverageData >= 38X + There is a 0.31% of reference with a coverageData >= 39X + There is a 0% of reference with a coverageData >= 40X + There is a 0% of reference with a coverageData >= 41X + There is a 0% of reference with a coverageData >= 42X + There is a 0% of reference with a coverageData >= 43X + There is a 0% of reference with a coverageData >= 44X + There is a 0% of reference with a coverageData >= 45X + There is a 0% of reference with a coverageData >= 46X + There is a 0% of reference with a coverageData >= 47X + There is a 0% of reference with a coverageData >= 48X + There is a 0% of reference with a coverageData >= 49X + There is a 0% of reference with a coverageData >= 50X + There is a 0% of reference with a coverageData >= 51X + + +>>>>>>> Coverage per contig + + test_chromosome 650 12665 19.484615384615385 16.581284452141826 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results_inside_features.txt Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,128 @@ +BamQC report +----------------------------------- + +>>>>>>> Input + + bam file = /tmp/tmpB4Sf0A/files/e/d/7/dataset_ed7510d4-c8f3-41fc-8cc1-3b854d9bdf14.dat + outfile = results/genome_results.txt + + +>>>>>>> Reference + + number of bases = 650 bp + number of contigs = 1 + + +>>>>>>> Globals + + number of windows = 325 + + number of reads = 100 + number of mapped reads = 100 (100%) + number of secondary alignments = 1 + + number of mapped bases = 6,451 bp + number of sequenced bases = 5,101 bp + number of aligned bases = 0 bp + number of duplicated reads (estimated) = 14 + duplication rate = 16.18% + + +>>>>>>> Globals inside + + regions size = 300 (46.15%) + number of mapped reads = 82 (82%) + + +>>>>>>> Insert size + + mean insert size = 0 + std insert size = 0 + median insert size = 0 + + +>>>>>>> Mapping quality + + mean mapping quality = 251.3687 + + +>>>>>>> ACTG content + + number of A's = 1,243 bp (24.37%) + number of C's = 1,257 bp (24.64%) + number of T's = 985 bp (19.31%) + number of G's = 1,616 bp (31.68%) + number of N's = 0 bp (0%) + + GC percentage = 56.32% + + +>>>>>>> Mismatches and indels + + general error rate = 0.0211 + number of mismatches = 136 + + +>>>>>>> Coverage + + mean coverageData = 21.5033X + std coverageData = 15.658X + + There is a 66% of reference with a coverageData >= 1X + There is a 65.33% of reference with a coverageData >= 2X + There is a 65% of reference with a coverageData >= 3X + There is a 64.33% of reference with a coverageData >= 4X + There is a 63.33% of reference with a coverageData >= 5X + There is a 59.67% of reference with a coverageData >= 6X + There is a 57.67% of reference with a coverageData >= 7X + There is a 57.67% of reference with a coverageData >= 8X + There is a 56% of reference with a coverageData >= 9X + There is a 55% of reference with a coverageData >= 10X + There is a 54.33% of reference with a coverageData >= 11X + There is a 54% of reference with a coverageData >= 12X + There is a 53.33% of reference with a coverageData >= 13X + There is a 53% of reference with a coverageData >= 14X + There is a 52.33% of reference with a coverageData >= 15X + There is a 52.33% of reference with a coverageData >= 16X + There is a 51.67% of reference with a coverageData >= 17X + There is a 51% of reference with a coverageData >= 18X + There is a 50% of reference with a coverageData >= 19X + There is a 50% of reference with a coverageData >= 20X + There is a 50% of reference with a coverageData >= 21X + There is a 49.67% of reference with a coverageData >= 22X + There is a 49.33% of reference with a coverageData >= 23X + There is a 48.33% of reference with a coverageData >= 24X + There is a 48% of reference with a coverageData >= 25X + There is a 45.33% of reference with a coverageData >= 26X + There is a 43% of reference with a coverageData >= 27X + There is a 42% of reference with a coverageData >= 28X + There is a 39.33% of reference with a coverageData >= 29X + There is a 35.67% of reference with a coverageData >= 30X + There is a 32.33% of reference with a coverageData >= 31X + There is a 25.67% of reference with a coverageData >= 32X + There is a 16.67% of reference with a coverageData >= 33X + There is a 13% of reference with a coverageData >= 34X + There is a 11.33% of reference with a coverageData >= 35X + There is a 10% of reference with a coverageData >= 36X + There is a 5.67% of reference with a coverageData >= 37X + There is a 3% of reference with a coverageData >= 38X + There is a 0% of reference with a coverageData >= 39X + There is a 0% of reference with a coverageData >= 40X + There is a 0% of reference with a coverageData >= 41X + There is a 0% of reference with a coverageData >= 42X + There is a 0% of reference with a coverageData >= 43X + There is a 0% of reference with a coverageData >= 44X + There is a 0% of reference with a coverageData >= 45X + There is a 0% of reference with a coverageData >= 46X + There is a 0% of reference with a coverageData >= 47X + There is a 0% of reference with a coverageData >= 48X + There is a 0% of reference with a coverageData >= 49X + There is a 0% of reference with a coverageData >= 50X + There is a 0% of reference with a coverageData >= 51X + + +>>>>>>> Coverage per contig + + test_chromosome 300 6451 21.503333333333334 15.658011438947867 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results_outside_features.txt Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,128 @@ +BamQC report +----------------------------------- + +>>>>>>> Input + + bam file = /tmp/tmprT4oZK/files/6/4/1/dataset_6416c0ca-3ecd-4273-ae01-22f2ac60965d.dat + outfile = results/outside_results.txt + + +>>>>>>> Reference + + number of bases = 650 bp + number of contigs = 1 + + +>>>>>>> Globals + + number of windows = 325 + + number of reads = 100 + number of mapped reads = 100 (100%) + number of secondary alignments = 1 + + number of mapped bases = 6,214 bp + number of sequenced bases = 2,364 bp + number of aligned bases = 0 bp + number of duplicated reads (estimated) = 4 + duplication rate = 14.29% + + +>>>>>>> Globals outside + + regions size = 350 (53.85%) + number of mapped reads = 18 (18%) + + +>>>>>>> Insert size + + mean insert size = 0 + std insert size = 0 + median insert size = 0 + + +>>>>>>> Mapping quality + + mean mapping quality = 255 + + +>>>>>>> ACTG content + + number of A's = 667 bp (28.21%) + number of C's = 645 bp (27.28%) + number of T's = 512 bp (21.66%) + number of G's = 540 bp (22.84%) + number of N's = 0 bp (0%) + + GC percentage = 50.13% + + +>>>>>>> Mismatches and indels + + general error rate = 0.0021 + number of mismatches = 13 + + +>>>>>>> Coverage + + mean coverageData = 17.7543X + std coverageData = 16.4764X + + There is a 10.58% of reference with a coverageData >= 1X + There is a 10.58% of reference with a coverageData >= 2X + There is a 10.58% of reference with a coverageData >= 3X + There is a 10.58% of reference with a coverageData >= 4X + There is a 10.58% of reference with a coverageData >= 5X + There is a 10.58% of reference with a coverageData >= 6X + There is a 10.58% of reference with a coverageData >= 7X + There is a 10.58% of reference with a coverageData >= 8X + There is a 10.58% of reference with a coverageData >= 9X + There is a 10.58% of reference with a coverageData >= 10X + There is a 10.58% of reference with a coverageData >= 11X + There is a 10.58% of reference with a coverageData >= 12X + There is a 10.58% of reference with a coverageData >= 13X + There is a 10.58% of reference with a coverageData >= 14X + There is a 10.58% of reference with a coverageData >= 15X + There is a 10.58% of reference with a coverageData >= 16X + There is a 10.58% of reference with a coverageData >= 17X + There is a 10.58% of reference with a coverageData >= 18X + There is a 10.58% of reference with a coverageData >= 19X + There is a 10.58% of reference with a coverageData >= 20X + There is a 10.58% of reference with a coverageData >= 21X + There is a 10.58% of reference with a coverageData >= 22X + There is a 10.58% of reference with a coverageData >= 23X + There is a 10.58% of reference with a coverageData >= 24X + There is a 10.58% of reference with a coverageData >= 25X + There is a 10.58% of reference with a coverageData >= 26X + There is a 10.58% of reference with a coverageData >= 27X + There is a 10.58% of reference with a coverageData >= 28X + There is a 10.58% of reference with a coverageData >= 29X + There is a 10.58% of reference with a coverageData >= 30X + There is a 10.58% of reference with a coverageData >= 31X + There is a 10.1% of reference with a coverageData >= 32X + There is a 9.62% of reference with a coverageData >= 33X + There is a 9.13% of reference with a coverageData >= 34X + There is a 7.21% of reference with a coverageData >= 35X + There is a 5.29% of reference with a coverageData >= 36X + There is a 3.37% of reference with a coverageData >= 37X + There is a 1.44% of reference with a coverageData >= 38X + There is a 0.96% of reference with a coverageData >= 39X + There is a 0% of reference with a coverageData >= 40X + There is a 0% of reference with a coverageData >= 41X + There is a 0% of reference with a coverageData >= 42X + There is a 0% of reference with a coverageData >= 43X + There is a 0% of reference with a coverageData >= 44X + There is a 0% of reference with a coverageData >= 45X + There is a 0% of reference with a coverageData >= 46X + There is a 0% of reference with a coverageData >= 47X + There is a 0% of reference with a coverageData >= 48X + There is a 0% of reference with a coverageData >= 49X + There is a 0% of reference with a coverageData >= 50X + There is a 0% of reference with a coverageData >= 51X + + +>>>>>>> Coverage per contig + + test_chromosome 4424 6214 1.404611211573237 3.9981701358234454 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapped_reads_clipping_profile.txt Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,76 @@ +#Read position (bp) Clipping profile +0.0 16.666666666666664 +1.0 5.555555555555555 +2.0 0.0 +3.0 0.0 +4.0 0.0 +5.0 0.0 +6.0 0.0 +7.0 0.0 +8.0 0.0 +9.0 0.0 +10.0 0.0 +11.0 0.0 +12.0 0.0 +13.0 0.0 +14.0 0.0 +15.0 0.0 +16.0 0.0 +17.0 0.0 +18.0 0.0 +19.0 0.0 +20.0 0.0 +21.0 0.0 +22.0 0.0 +23.0 0.0 +24.0 0.0 +25.0 0.0 +26.0 0.0 +27.0 0.0 +28.0 0.0 +29.0 0.0 +30.0 0.0 +31.0 0.0 +32.0 0.0 +33.0 0.0 +34.0 0.0 +35.0 0.0 +36.0 0.0 +37.0 0.0 +38.0 0.0 +39.0 0.0 +40.0 0.0 +41.0 0.0 +42.0 0.0 +43.0 0.0 +44.0 0.0 +45.0 0.0 +46.0 0.0 +47.0 0.0 +48.0 0.0 +49.0 0.0 +50.0 0.0 +51.0 0.0 +52.0 0.0 +53.0 0.0 +54.0 0.0 +55.0 0.0 +56.0 0.0 +57.0 0.0 +58.0 0.0 +59.0 0.0 +60.0 0.0 +61.0 0.0 +62.0 0.0 +63.0 0.0 +64.0 0.0 +65.0 0.0 +66.0 0.0 +67.0 0.0 +68.0 0.0 +69.0 0.0 +70.0 0.0 +71.0 5.555555555555555 +72.0 11.11111111111111 +73.0 16.666666666666664 +74.0 44.44444444444444
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapped_reads_gc-content_distribution.txt Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,101 @@ +#GC Content (%) Sample HUMAN (hg19) +1.0 0.0 0.0 +2.0 0.0 3.0E-6 +3.0 0.0 3.0E-6 +4.0 0.0 1.0E-5 +5.0 0.0 8.0E-6 +6.0 0.0 1.2000000000000002E-5 +7.0 0.0 6.999999999999999E-6 +8.0 0.0 9.999999999999999E-6 +9.0 0.0 1.6E-5 +10.0 0.0 1.5000000000000002E-5 +11.0 0.0 1.9999999999999998E-5 +12.0 0.0 1.6E-5 +13.0 0.0 1.6E-5 +14.0 0.0 2.4999999999999998E-5 +15.0 0.0 2.2000000000000003E-5 +16.0 0.0 2.6999999999999996E-5 +17.0 0.0 3.3E-5 +18.0 0.0 3.7000000000000005E-5 +19.0 0.0 4.7000000000000004E-5 +20.0 0.0 5.4999999999999995E-5 +21.0 0.0 6.400000000000001E-5 +22.0 0.0 9.3E-5 +23.0 0.0 1.66E-4 +24.0 0.0 3.03E-4 +25.0 0.0 7.059999999999999E-4 +26.0 0.0 0.0016020000000000001 +27.0 0.0 0.0033690000000000005 +28.0 0.0 0.006167999999999999 +29.0 0.0 0.010352 +30.0 0.0 0.015647 +31.0 0.0 0.022148 +32.0 0.0 0.028808 +33.0 0.0 0.035106000000000005 +34.0 0.0 0.041161 +35.0 0.0 0.047408 +36.0 0.0 0.052698999999999996 +37.0 0.0 0.057517000000000006 +38.0 0.0 0.061487999999999994 +39.0 0.0 0.063321 +40.0 0.0 0.060248 +41.0 0.0 0.055508 +42.0 0.0 0.051446000000000006 +43.0 0.0 0.048194 +44.0 0.017857142857142856 0.044423 +45.0 0.0 0.040655000000000004 +46.0 0.03571428571428571 0.03652 +47.0 0.0 0.032315 +48.0 0.017857142857142856 0.028137999999999996 +49.0 0.0 0.02458 +50.0 0.017857142857142856 0.020810000000000002 +51.0 0.0 0.017532 +52.0 0.05357142857142857 0.014506999999999997 +53.0 0.017857142857142856 0.012007 +54.0 0.14285714285714285 0.010018 +55.0 0.08928571428571429 0.008414999999999999 +56.0 0.17857142857142855 0.007258 +57.0 0.03571428571428571 0.006174999999999999 +58.0 0.08928571428571429 0.005363000000000001 +59.0 0.03571428571428571 0.0046159999999999994 +60.0 0.14285714285714285 0.003946 +61.0 0.0 0.0034579999999999993 +62.0 0.03571428571428571 0.002915 +63.0 0.017857142857142856 0.0024610000000000005 +64.0 0.05357142857142857 0.0019950000000000002 +65.0 0.0 0.0016779999999999998 +66.0 0.017857142857142856 0.0013500000000000003 +67.0 0.0 0.001069 +68.0 0.0 8.119999999999999E-4 +69.0 0.0 6.4E-4 +70.0 0.0 5.05E-4 +71.0 0.0 4.0299999999999993E-4 +72.0 0.0 3.2E-4 +73.0 0.0 2.79E-4 +74.0 0.0 2.0700000000000002E-4 +75.0 0.0 2.0099999999999998E-4 +76.0 0.0 1.54E-4 +77.0 0.0 1.12E-4 +78.0 0.0 7.699999999999999E-5 +79.0 0.0 6.3E-5 +80.0 0.0 3.7E-5 +81.0 0.0 2.8000000000000003E-5 +82.0 0.0 1.6E-5 +83.0 0.0 9.0E-6 +84.0 0.0 4.0E-6 +85.0 0.0 0.0 +86.0 0.0 1.0E-6 +87.0 0.0 0.0 +88.0 0.0 0.0 +89.0 0.0 0.0 +90.0 0.0 0.0 +91.0 0.0 0.0 +92.0 0.0 0.0 +93.0 0.0 0.0 +94.0 0.0 0.0 +95.0 0.0 0.0 +96.0 0.0 0.0 +97.0 0.0 0.0 +98.0 0.0 0.0 +99.0 0.0 0.0 +100.0 0.0 0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapped_reads_nucleotide_content.txt Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,76 @@ +# Position (bp) A C G T N +0.0 34.177215189873415 21.518987341772153 26.582278481012654 17.72151898734177 0.0 +1.0 23.456790123456788 33.33333333333333 20.98765432098765 22.22222222222222 0.0 +2.0 25.609756097560975 20.73170731707317 35.36585365853659 18.29268292682927 0.0 +3.0 23.170731707317074 28.04878048780488 28.04878048780488 20.73170731707317 0.0 +4.0 31.70731707317073 26.82926829268293 24.390243902439025 17.073170731707318 0.0 +5.0 25.609756097560975 19.51219512195122 34.146341463414636 20.73170731707317 0.0 +6.0 25.609756097560975 23.170731707317074 34.146341463414636 17.073170731707318 0.0 +7.0 28.04878048780488 21.951219512195124 30.48780487804878 19.51219512195122 0.0 +8.0 23.170731707317074 18.29268292682927 39.02439024390244 19.51219512195122 0.0 +9.0 28.04878048780488 29.268292682926827 24.390243902439025 18.29268292682927 0.0 +10.0 24.390243902439025 23.170731707317074 34.146341463414636 18.29268292682927 0.0 +11.0 19.51219512195122 31.70731707317073 28.04878048780488 20.73170731707317 0.0 +12.0 34.146341463414636 23.170731707317074 28.04878048780488 14.634146341463413 0.0 +13.0 26.82926829268293 18.29268292682927 36.58536585365854 18.29268292682927 0.0 +14.0 24.390243902439025 26.82926829268293 29.268292682926827 19.51219512195122 0.0 +15.0 29.268292682926827 21.951219512195124 28.04878048780488 20.73170731707317 0.0 +16.0 31.70731707317073 25.609756097560975 29.268292682926827 13.414634146341465 0.0 +17.0 15.853658536585366 25.609756097560975 35.36585365853659 23.170731707317074 0.0 +18.0 31.70731707317073 17.073170731707318 31.70731707317073 19.51219512195122 0.0 +19.0 24.390243902439025 29.268292682926827 29.268292682926827 17.073170731707318 0.0 +20.0 21.951219512195124 25.609756097560975 29.268292682926827 23.170731707317074 0.0 +21.0 23.170731707317074 28.04878048780488 36.58536585365854 12.195121951219512 0.0 +22.0 28.04878048780488 30.48780487804878 18.29268292682927 23.170731707317074 0.0 +23.0 23.170731707317074 18.29268292682927 29.268292682926827 29.268292682926827 0.0 +24.0 25.609756097560975 19.51219512195122 35.36585365853659 19.51219512195122 0.0 +25.0 23.170731707317074 26.82926829268293 25.609756097560975 24.390243902439025 0.0 +26.0 21.951219512195124 19.51219512195122 41.46341463414634 17.073170731707318 0.0 +27.0 18.29268292682927 29.268292682926827 35.36585365853659 17.073170731707318 0.0 +28.0 29.268292682926827 30.48780487804878 25.609756097560975 14.634146341463413 0.0 +29.0 17.073170731707318 25.609756097560975 36.58536585365854 20.73170731707317 0.0 +30.0 25.609756097560975 21.951219512195124 32.926829268292686 19.51219512195122 0.0 +31.0 29.268292682926827 23.170731707317074 32.926829268292686 14.634146341463413 0.0 +32.0 29.268292682926827 21.951219512195124 24.390243902439025 24.390243902439025 0.0 +33.0 20.73170731707317 31.70731707317073 26.82926829268293 20.73170731707317 0.0 +34.0 18.29268292682927 20.73170731707317 40.243902439024396 20.73170731707317 0.0 +35.0 37.80487804878049 13.414634146341465 28.04878048780488 20.73170731707317 0.0 +36.0 28.04878048780488 28.04878048780488 28.04878048780488 15.853658536585366 0.0 +37.0 21.951219512195124 20.73170731707317 39.02439024390244 18.29268292682927 0.0 +38.0 34.146341463414636 26.82926829268293 14.634146341463413 24.390243902439025 0.0 +39.0 31.70731707317073 17.073170731707318 26.82926829268293 24.390243902439025 0.0 +40.0 26.82926829268293 24.390243902439025 31.70731707317073 17.073170731707318 0.0 +41.0 30.48780487804878 19.51219512195122 25.609756097560975 24.390243902439025 0.0 +42.0 15.853658536585366 25.609756097560975 34.146341463414636 24.390243902439025 0.0 +43.0 29.268292682926827 24.390243902439025 28.04878048780488 18.29268292682927 0.0 +44.0 26.82926829268293 24.390243902439025 31.70731707317073 17.073170731707318 0.0 +45.0 29.268292682926827 23.170731707317074 29.268292682926827 18.29268292682927 0.0 +46.0 24.390243902439025 23.170731707317074 30.48780487804878 21.951219512195124 0.0 +47.0 25.609756097560975 28.04878048780488 30.48780487804878 15.853658536585366 0.0 +48.0 29.268292682926827 25.609756097560975 29.268292682926827 15.853658536585366 0.0 +49.0 23.170731707317074 23.170731707317074 32.926829268292686 20.73170731707317 0.0 +50.0 24.390243902439025 28.04878048780488 31.70731707317073 15.853658536585366 0.0 +51.0 24.390243902439025 24.390243902439025 31.70731707317073 19.51219512195122 0.0 +52.0 18.29268292682927 26.82926829268293 34.146341463414636 20.73170731707317 0.0 +53.0 26.82926829268293 23.170731707317074 36.58536585365854 13.414634146341465 0.0 +54.0 26.82926829268293 23.170731707317074 31.70731707317073 18.29268292682927 0.0 +55.0 25.609756097560975 26.82926829268293 28.04878048780488 19.51219512195122 0.0 +56.0 10.975609756097562 32.926829268292686 40.243902439024396 15.853658536585366 0.0 +57.0 26.82926829268293 19.51219512195122 29.268292682926827 24.390243902439025 0.0 +58.0 26.82926829268293 30.48780487804878 25.609756097560975 17.073170731707318 0.0 +59.0 21.951219512195124 19.51219512195122 32.926829268292686 25.609756097560975 0.0 +60.0 20.73170731707317 28.04878048780488 32.926829268292686 18.29268292682927 0.0 +61.0 30.48780487804878 19.51219512195122 32.926829268292686 17.073170731707318 0.0 +62.0 24.390243902439025 23.170731707317074 30.48780487804878 21.951219512195124 0.0 +63.0 19.51219512195122 23.170731707317074 29.268292682926827 28.04878048780488 0.0 +64.0 25.609756097560975 31.70731707317073 24.390243902439025 18.29268292682927 0.0 +65.0 18.29268292682927 24.390243902439025 30.48780487804878 26.82926829268293 0.0 +66.0 20.73170731707317 19.51219512195122 36.58536585365854 23.170731707317074 0.0 +67.0 23.170731707317074 31.70731707317073 25.609756097560975 19.51219512195122 0.0 +68.0 15.853658536585366 24.390243902439025 42.68292682926829 17.073170731707318 0.0 +69.0 25.609756097560975 26.82926829268293 29.268292682926827 18.29268292682927 0.0 +70.0 24.390243902439025 34.146341463414636 31.70731707317073 9.75609756097561 0.0 +71.0 19.753086419753085 27.160493827160494 29.629629629629626 23.456790123456788 0.0 +72.0 25.0 37.5 17.5 20.0 0.0 +73.0 24.050632911392405 20.253164556962027 34.177215189873415 21.518987341772153 0.0 +74.0 17.56756756756757 31.08108108108108 28.37837837837838 22.972972972972975 0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapping_quality_across_reference.txt Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,326 @@ +#Position (bp) mapping quality +1.5 0.0 +3.5 0.0 +5.5 0.0 +7.5 0.0 +9.5 0.0 +11.5 0.0 +13.5 0.0 +15.5 0.0 +17.5 0.0 +19.5 0.0 +21.5 0.0 +23.5 0.0 +25.5 0.0 +27.5 0.0 +29.5 0.0 +31.5 0.0 +33.5 0.0 +35.5 0.0 +37.5 0.0 +39.5 0.0 +41.5 0.0 +43.5 0.0 +45.5 0.0 +47.5 0.0 +49.5 0.0 +51.5 0.0 +53.5 255.0 +55.5 255.0 +57.5 255.0 +59.5 255.0 +61.5 255.0 +63.5 255.0 +65.5 255.0 +67.5 255.0 +69.5 255.0 +71.5 255.0 +73.5 255.0 +75.5 255.0 +77.5 255.0 +79.5 255.0 +81.5 255.0 +83.5 255.0 +85.5 255.0 +87.5 255.0 +89.5 255.0 +91.5 236.33333333333334 +93.5 238.2 +95.5 239.72727272727272 +97.5 240.6 +99.5 241.0 +101.5 243.27906976744185 +103.5 244.04347826086956 +105.5 244.27659574468086 +107.5 244.92 +109.5 244.92 +111.5 244.92 +113.5 244.92 +115.5 245.30769230769232 +117.5 245.30769230769232 +119.5 245.30769230769232 +121.5 245.49056603773585 +123.5 246.31034482758622 +125.5 247.125 +127.5 247.36363636363637 +129.5 247.24615384615385 +131.5 247.24615384615385 +133.5 247.125 +135.5 247.47761194029852 +137.5 247.36363636363637 +139.5 247.58823529411765 +141.5 248.0 +143.5 248.28 +145.5 248.3684210526316 +147.5 248.3684210526316 +149.5 248.3684210526316 +151.5 248.3684210526316 +153.5 248.0 +155.5 248.1891891891892 +157.5 248.0958904109589 +159.5 248.0958904109589 +161.5 248.0958904109589 +163.5 247.90140845070422 +165.5 251.54794520547946 +167.5 255.0 +169.5 255.0 +171.5 255.0 +173.5 255.0 +175.5 255.0 +177.5 255.0 +179.5 255.0 +181.5 255.0 +183.5 255.0 +185.5 255.0 +187.5 255.0 +189.5 255.0 +191.5 255.0 +193.5 255.0 +195.5 255.0 +197.5 255.0 +199.5 255.0 +201.5 255.0 +203.5 255.0 +205.5 255.0 +207.5 255.0 +209.5 255.0 +211.5 255.0 +213.5 255.0 +215.5 255.0 +217.5 255.0 +219.5 255.0 +221.5 255.0 +223.5 255.0 +225.5 255.0 +227.5 255.0 +229.5 255.0 +231.5 255.0 +233.5 255.0 +235.5 255.0 +237.5 255.0 +239.5 255.0 +241.5 255.0 +243.5 255.0 +245.5 255.0 +247.5 255.0 +249.5 255.0 +251.5 0.0 +253.5 0.0 +255.5 0.0 +257.5 0.0 +259.5 0.0 +261.5 0.0 +263.5 0.0 +265.5 0.0 +267.5 0.0 +269.5 0.0 +271.5 0.0 +273.5 0.0 +275.5 0.0 +277.5 0.0 +279.5 0.0 +281.5 0.0 +283.5 0.0 +285.5 0.0 +287.5 0.0 +289.5 0.0 +291.5 0.0 +293.5 0.0 +295.5 0.0 +297.5 0.0 +299.5 0.0 +301.5 0.0 +303.5 0.0 +305.5 0.0 +307.5 0.0 +309.5 0.0 +311.5 0.0 +313.5 0.0 +315.5 0.0 +317.5 0.0 +319.5 0.0 +321.5 0.0 +323.5 0.0 +325.5 0.0 +327.5 0.0 +329.5 0.0 +331.5 0.0 +333.5 0.0 +335.5 0.0 +337.5 0.0 +339.5 0.0 +341.5 0.0 +343.5 0.0 +345.5 0.0 +347.5 0.0 +349.5 0.0 +351.5 0.0 +353.5 0.0 +355.5 0.0 +357.5 0.0 +359.5 0.0 +361.5 0.0 +363.5 0.0 +365.5 0.0 +367.5 0.0 +369.5 0.0 +371.5 0.0 +373.5 0.0 +375.5 0.0 +377.5 0.0 +379.5 0.0 +381.5 0.0 +383.5 0.0 +385.5 0.0 +387.5 0.0 +389.5 0.0 +391.5 0.0 +393.5 0.0 +395.5 0.0 +397.5 0.0 +399.5 0.0 +401.5 0.0 +403.5 0.0 +405.5 0.0 +407.5 0.0 +409.5 0.0 +411.5 0.0 +413.5 0.0 +415.5 0.0 +417.5 0.0 +419.5 0.0 +421.5 0.0 +423.5 0.0 +425.5 0.0 +427.5 0.0 +429.5 0.0 +431.5 0.0 +433.5 0.0 +435.5 0.0 +437.5 0.0 +439.5 0.0 +441.5 0.0 +443.5 0.0 +445.5 0.0 +447.5 0.0 +449.5 0.0 +451.5 0.0 +453.5 0.0 +455.5 0.0 +457.5 0.0 +459.5 0.0 +461.5 0.0 +463.5 0.0 +465.5 0.0 +467.5 0.0 +469.5 0.0 +471.5 0.0 +473.5 0.0 +475.5 0.0 +477.5 0.0 +479.5 0.0 +481.5 0.0 +483.5 0.0 +485.5 0.0 +487.5 0.0 +489.5 0.0 +491.5 0.0 +493.5 0.0 +495.5 0.0 +497.5 0.0 +499.5 0.0 +501.5 0.0 +503.5 0.0 +505.5 0.0 +507.5 0.0 +509.5 0.0 +511.5 0.0 +513.5 0.0 +515.5 0.0 +517.5 0.0 +519.5 0.0 +521.5 0.0 +523.5 0.0 +525.5 0.0 +527.5 0.0 +529.5 0.0 +531.5 0.0 +533.5 0.0 +535.5 0.0 +537.5 0.0 +539.5 0.0 +541.5 0.0 +543.5 0.0 +545.5 0.0 +547.5 0.0 +549.5 0.0 +551.5 0.0 +553.5 0.0 +555.5 0.0 +557.5 0.0 +559.5 0.0 +561.5 0.0 +563.5 0.0 +565.5 0.0 +567.5 0.0 +569.5 0.0 +571.5 0.0 +573.5 0.0 +575.5 0.0 +577.5 0.0 +579.5 0.0 +581.5 0.0 +583.5 0.0 +585.5 0.0 +587.5 0.0 +589.5 0.0 +591.5 0.0 +593.5 0.0 +595.5 0.0 +597.5 0.0 +599.5 0.0 +601.5 0.0 +603.5 0.0 +605.5 0.0 +607.5 0.0 +609.5 0.0 +611.5 0.0 +613.5 0.0 +615.5 0.0 +617.5 0.0 +619.5 0.0 +621.5 0.0 +623.5 0.0 +625.5 0.0 +627.5 0.0 +629.5 0.0 +631.5 0.0 +633.5 0.0 +635.5 0.0 +637.5 0.0 +639.5 0.0 +641.5 0.0 +643.5 0.0 +645.5 0.0 +647.5 0.0 +649.5 0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapping_quality_histogram.txt Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,13 @@ +#Mapping quality mapping quality +235.0 1.0 +237.0 2.0 +239.0 2.0 +240.0 2.0 +241.0 3.0 +243.0 2.0 +244.0 12.0 +245.0 8.0 +246.0 2.0 +247.0 18.0 +248.0 23.0 +255.0 123.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mouse_counts_ensemble_1000_6.tsv Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,1000 @@ +#gene -GlcN01 -GlcN02 -GlcN03 +GlcN01 +GlcN02 +GlcN03 +ENSMUSG00000085214 641 542 776 491 791 368 +ENSMUSG00000096956 73 17 47 32 29 63 +ENSMUSG00000021252 2359 1563 2497 2126 2149 1296 +ENSMUSG00000046840 39 165 124 83 144 31 +ENSMUSG00000044062 1 0 3 6 1 0 +ENSMUSG00000007777 292 184 220 228 237 270 +ENSMUSG00000037361 421 300 380 316 393 310 +ENSMUSG00000043644 16 5 7 6 6 8 +ENSMUSG00000024442 812 566 727 569 784 692 +ENSMUSG00000042208 445 273 375 305 410 399 +ENSMUSG00000020831 5 4 5 6 6 3 +ENSMUSG00000025731 1259 942 1113 888 1585 1076 +ENSMUSG00000096232 394 309 396 261 417 306 +ENSMUSG00000055312 53 53 59 43 63 35 +ENSMUSG00000058706 948 581 835 716 927 622 +ENSMUSG00000001418 1440 813 1052 1092 1044 1168 +ENSMUSG00000028608 305 208 262 229 273 225 +ENSMUSG00000089900 3 3 2 7 4 5 +ENSMUSG00000058812 51 30 45 41 32 35 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/per_base_coverage_default.txt Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,299 @@ +#chr pos coverage +test_chromosome 53 1 +test_chromosome 54 1 +test_chromosome 55 2 +test_chromosome 56 3 +test_chromosome 57 3 +test_chromosome 58 4 +test_chromosome 59 4 +test_chromosome 60 4 +test_chromosome 61 5 +test_chromosome 62 5 +test_chromosome 63 5 +test_chromosome 64 5 +test_chromosome 65 5 +test_chromosome 66 5 +test_chromosome 67 5 +test_chromosome 68 5 +test_chromosome 69 5 +test_chromosome 70 5 +test_chromosome 71 5 +test_chromosome 72 6 +test_chromosome 73 6 +test_chromosome 74 6 +test_chromosome 75 6 +test_chromosome 76 6 +test_chromosome 77 6 +test_chromosome 78 8 +test_chromosome 79 8 +test_chromosome 80 8 +test_chromosome 81 8 +test_chromosome 82 8 +test_chromosome 83 9 +test_chromosome 84 9 +test_chromosome 85 9 +test_chromosome 86 10 +test_chromosome 87 10 +test_chromosome 88 11 +test_chromosome 89 12 +test_chromosome 90 12 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/per_base_coverage_inside_features.txt Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,199 @@ +#chr pos coverage +test_chromosome 53 1 +test_chromosome 54 1 +test_chromosome 55 2 +test_chromosome 56 3 +test_chromosome 57 3 +test_chromosome 58 4 +test_chromosome 59 4 +test_chromosome 60 4 +test_chromosome 61 5 +test_chromosome 62 5 +test_chromosome 63 5 +test_chromosome 64 5 +test_chromosome 65 5 +test_chromosome 66 5 +test_chromosome 67 5 +test_chromosome 68 5 +test_chromosome 69 5 +test_chromosome 70 5 +test_chromosome 71 5 +test_chromosome 72 6 +test_chromosome 73 6 +test_chromosome 74 6 +test_chromosome 75 6 +test_chromosome 76 6 +test_chromosome 77 6 +test_chromosome 78 8 +test_chromosome 79 8 +test_chromosome 80 8 +test_chromosome 81 8 +test_chromosome 82 8 +test_chromosome 83 9 +test_chromosome 84 9 +test_chromosome 85 9 +test_chromosome 86 10 +test_chromosome 87 10 +test_chromosome 88 11 +test_chromosome 89 12 +test_chromosome 90 12 +test_chromosome 91 13 +test_chromosome 92 14 +test_chromosome 93 14 +test_chromosome 94 16 +test_chromosome 95 16 +test_chromosome 96 17 +test_chromosome 97 17 +test_chromosome 98 18 +test_chromosome 99 18 +test_chromosome 100 18 +test_chromosome 101 21 +test_chromosome 102 22 +test_chromosome 103 23 +test_chromosome 104 23 +test_chromosome 105 23 +test_chromosome 106 24 +test_chromosome 107 25 +test_chromosome 108 25 +test_chromosome 109 25 +test_chromosome 110 25 +test_chromosome 111 25 +test_chromosome 112 25 +test_chromosome 113 25 +test_chromosome 114 25 +test_chromosome 115 26 +test_chromosome 116 26 +test_chromosome 117 26 +test_chromosome 118 26 +test_chromosome 119 26 +test_chromosome 120 26 +test_chromosome 121 26 +test_chromosome 122 27 +test_chromosome 123 29 +test_chromosome 124 29 +test_chromosome 125 32 +test_chromosome 126 32 +test_chromosome 127 33 +test_chromosome 128 33 +test_chromosome 129 33 +test_chromosome 130 32 +test_chromosome 131 32 +test_chromosome 132 33 +test_chromosome 133 32 +test_chromosome 134 32 +test_chromosome 135 34 +test_chromosome 136 33 +test_chromosome 137 33 +test_chromosome 138 33 +test_chromosome 139 34 +test_chromosome 140 34 +test_chromosome 141 35 +test_chromosome 142 37 +test_chromosome 143 37 +test_chromosome 144 38 +test_chromosome 145 38 +test_chromosome 146 38 +test_chromosome 147 38 +test_chromosome 148 38 +test_chromosome 149 38 +test_chromosome 150 38 +test_chromosome 151 38 +test_chromosome 152 38 +test_chromosome 153 36 +test_chromosome 154 36 +test_chromosome 155 37 +test_chromosome 156 37 +test_chromosome 157 37 +test_chromosome 158 36 +test_chromosome 159 36 +test_chromosome 160 37 +test_chromosome 161 36 +test_chromosome 162 37 +test_chromosome 163 36 +test_chromosome 164 35 +test_chromosome 165 37 +test_chromosome 166 36 +test_chromosome 167 36 +test_chromosome 168 36 +test_chromosome 169 34 +test_chromosome 170 36 +test_chromosome 171 36 +test_chromosome 172 36 +test_chromosome 173 35 +test_chromosome 174 35 +test_chromosome 175 36 +test_chromosome 176 33 +test_chromosome 177 32 +test_chromosome 178 32 +test_chromosome 179 32 +test_chromosome 180 32 +test_chromosome 181 32 +test_chromosome 182 31 +test_chromosome 183 31 +test_chromosome 184 32 +test_chromosome 185 32 +test_chromosome 186 32 +test_chromosome 187 32 +test_chromosome 188 32 +test_chromosome 189 32 +test_chromosome 190 31 +test_chromosome 191 31 +test_chromosome 192 31 +test_chromosome 193 31 +test_chromosome 194 32 +test_chromosome 195 32 +test_chromosome 196 32 +test_chromosome 197 32 +test_chromosome 198 30 +test_chromosome 199 29 +test_chromosome 200 28 +test_chromosome 201 31 +test_chromosome 202 30 +test_chromosome 203 29 +test_chromosome 204 30 +test_chromosome 205 31 +test_chromosome 206 31 +test_chromosome 207 31 +test_chromosome 208 32 +test_chromosome 209 31 +test_chromosome 210 31 +test_chromosome 211 31 +test_chromosome 212 31 +test_chromosome 213 31 +test_chromosome 214 31 +test_chromosome 215 31 +test_chromosome 216 30 +test_chromosome 217 28 +test_chromosome 218 28 +test_chromosome 219 27 +test_chromosome 220 27 +test_chromosome 221 28 +test_chromosome 222 28 +test_chromosome 223 28 +test_chromosome 224 28 +test_chromosome 225 29 +test_chromosome 226 29 +test_chromosome 227 30 +test_chromosome 228 30 +test_chromosome 229 31 +test_chromosome 230 30 +test_chromosome 231 31 +test_chromosome 232 32 +test_chromosome 233 33 +test_chromosome 234 34 +test_chromosome 235 33 +test_chromosome 236 33 +test_chromosome 237 32 +test_chromosome 238 32 +test_chromosome 239 32 +test_chromosome 240 30 +test_chromosome 241 30 +test_chromosome 242 29 +test_chromosome 243 31 +test_chromosome 244 32 +test_chromosome 245 30 +test_chromosome 246 29 +test_chromosome 247 29 +test_chromosome 248 29 +test_chromosome 249 29 +test_chromosome 250 28
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/per_base_coverage_outside_features.txt Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,101 @@ +#chr pos coverage +test_chromosome 351 31 +test_chromosome 352 32 +test_chromosome 353 33 +test_chromosome 354 34 +test_chromosome 355 35 +test_chromosome 356 34 +test_chromosome 357 34 +test_chromosome 358 35 +test_chromosome 359 34 +test_chromosome 360 35 +test_chromosome 361 35 +test_chromosome 362 36 +test_chromosome 363 36 +test_chromosome 364 36 +test_chromosome 365 36 +test_chromosome 366 37 +test_chromosome 367 37 +test_chromosome 368 37 +test_chromosome 369 37 +test_chromosome 370 36 +test_chromosome 371 37 +test_chromosome 372 37 +test_chromosome 373 39 +test_chromosome 374 39 +test_chromosome 375 38 +test_chromosome 376 36 +test_chromosome 377 36 +test_chromosome 378 36 +test_chromosome 379 36 +test_chromosome 380 34 +test_chromosome 381 33 +test_chromosome 382 32 +test_chromosome 383 32 +test_chromosome 384 31 +test_chromosome 385 31 +test_chromosome 386 31 +test_chromosome 387 31 +test_chromosome 388 31 +test_chromosome 389 30 +test_chromosome 390 30 +test_chromosome 391 30 +test_chromosome 392 30 +test_chromosome 393 30 +test_chromosome 394 30 +test_chromosome 395 30 +test_chromosome 396 29 +test_chromosome 397 28 +test_chromosome 398 28 +test_chromosome 399 28 +test_chromosome 400 27 +test_chromosome 501 25 +test_chromosome 502 25 +test_chromosome 503 25 +test_chromosome 504 25 +test_chromosome 505 25 +test_chromosome 506 24 +test_chromosome 507 23 +test_chromosome 508 22 +test_chromosome 509 21 +test_chromosome 510 21 +test_chromosome 511 21 +test_chromosome 512 21 +test_chromosome 513 21 +test_chromosome 514 21 +test_chromosome 515 21 +test_chromosome 516 21 +test_chromosome 517 20 +test_chromosome 518 18 +test_chromosome 519 17 +test_chromosome 520 17 +test_chromosome 521 17 +test_chromosome 522 16 +test_chromosome 523 15 +test_chromosome 524 15 +test_chromosome 525 14 +test_chromosome 526 14 +test_chromosome 527 13 +test_chromosome 528 12 +test_chromosome 529 11 +test_chromosome 530 10 +test_chromosome 531 10 +test_chromosome 532 10 +test_chromosome 533 9 +test_chromosome 534 9 +test_chromosome 535 8 +test_chromosome 536 8 +test_chromosome 537 7 +test_chromosome 538 7 +test_chromosome 539 7 +test_chromosome 540 7 +test_chromosome 541 6 +test_chromosome 542 6 +test_chromosome 543 6 +test_chromosome 544 5 +test_chromosome 545 5 +test_chromosome 546 4 +test_chromosome 547 4 +test_chromosome 548 2 +test_chromosome 549 2 +test_chromosome 550 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaseq_qc_counts_custom.txt Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,2 @@ +#GeneID try_this +GENE1 45
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaseq_qc_results_custom.txt Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,48 @@ +RNA-Seq QC report +----------------------------------- + +>>>>>>> Input + + bam file = /tmp/tmp_CFvEQ/files/000/dataset_49.dat + gff file = /tmp/tmp_CFvEQ/files/000/dataset_2.dat + counting algorithm = proportional + protocol = strand-specific-forward + + +>>>>>>> Reads alignment + + reads aligned (left/right) = 0 / 0 + read pairs aligned = 0 + total alignments = 101 + secondary alignments = 1 + non-unique alignments = 0 + aligned to genes = 46 + ambiguous alignments = 0 + no feature assigned = 55 + not aligned = 0 + + +>>>>>>> Reads genomic origin + + exonic = 46 (45.54%) + intronic = 0 (0%) + intergenic = 55 (54.46%) + overlapping exon = 0 (0%) + + +>>>>>>> Transcript coverage profile + + 5' bias = NaN + 3' bias = NaN + 5'-3' bias = NaN + + +>>>>>>> Junction analysis + + reads at junctions = 53 + + CTTT : 47.17% + CCAC : 47.17% + GCAC : 1.89% + CTAC : 1.89% + GAAT : 1.89%
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaseq_qc_results_default.txt Thu Oct 10 17:41:10 2019 -0400 @@ -0,0 +1,47 @@ +RNA-Seq QC report +----------------------------------- + +>>>>>>> Input + + bam file = /tmp/tmp_CFvEQ/files/000/dataset_1.dat + gff file = /tmp/tmp_CFvEQ/files/000/dataset_2.dat + counting algorithm = uniquely-mapped-reads + protocol = non-strand-specific + + +>>>>>>> Reads alignment + + reads aligned = 100 + total alignments = 101 + secondary alignments = 1 + non-unique alignments = 2 + aligned to genes = 54 + ambiguous alignments = 0 + no feature assigned = 45 + not aligned = 0 + SSP estimation (fwd/rev) = 0.59 / 0.41 + + +>>>>>>> Reads genomic origin + + exonic = 54 (54.55%) + intronic = 0 (0%) + intergenic = 45 (45.45%) + overlapping exon = 0 (0%) + + +>>>>>>> Transcript coverage profile + + 5' bias = NaN + 3' bias = NaN + 5'-3' bias = NaN + + +>>>>>>> Junction analysis + + reads at junctions = 52 + + CTTT : 48.08% + CCAC : 48.08% + GCAC : 1.92% + CTAC : 1.92%