Mercurial > repos > iuc > trinity_gene_to_trans_map
changeset 9:1b04880ff362 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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--- a/gene_to_trans_map.xml Mon Jan 22 11:27:24 2018 -0500 +++ b/gene_to_trans_map.xml Thu Jun 14 03:11:51 2018 -0400 @@ -1,11 +1,11 @@ -<tool id="trinity_gene_to_trans_map" name="Generate gene to transcript map" version="@WRAPPER_VERSION@.0"> +<tool id="trinity_gene_to_trans_map" name="Generate gene to transcript map" version="@WRAPPER_VERSION@"> <description>for Trinity assembly</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="aggressive"><![CDATA[ - get_Trinity_gene_to_trans_map.pl "$assembly" > "$map" + get_Trinity_gene_to_trans_map.pl '$assembly' > '$map' ]]></command> <inputs> <param format="fasta" name="assembly" type="data" label="Trinity assembly"/> @@ -23,6 +23,7 @@ Trinity_ assembles transcript sequences from Illumina RNA-Seq data. This tool produces a file containing correspondance between gene ids and transcript ids based on the name of transcripts assembled by Trinity. The output file is intended to be used by the "Align reads and estimate abundance" tool. + The same file is automatically generated when running Trinity, this tool is only intended to be used when you don't (or no longer) have access to the one produced by Trinity. .. _Trinity: http://trinityrnaseq.github.io </help>
--- a/macros.xml Mon Jan 22 11:27:24 2018 -0500 +++ b/macros.xml Thu Jun 14 03:11:51 2018 -0400 @@ -2,19 +2,19 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.4.0">trinity</requirement> + <requirement type="package" version="2.6.6">trinity</requirement> <yield/> </requirements> </xml> - <token name="@WRAPPER_VERSION@">2.4.0</token> + <token name="@WRAPPER_VERSION@">2.6.6</token> <token name="@COMMAND_PAIRED_STRAND_JACCARD@"> - #if $inputs.strand.is_strand_specific: - --SS_lib_type $inputs.strand.library_type + #if $pool.inputs.strand.is_strand_specific: + --SS_lib_type $pool.inputs.strand.library_type #end if - $inputs.jaccard_clip + $pool.inputs.jaccard_clip </token> <xml name="input_paired_strand_jaccard">
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/Trinity.map Thu Jun 14 03:11:51 2018 -0400 @@ -0,0 +1,7 @@ +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 +TRINITY_DN1_c0_g1 TRINITY_DN1_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/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.DE.subset.GOseq.enriched Thu Jun 14 03:11:51 2018 -0400 @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR
--- a/test-data/count/analyze_diff_expr/results.matrix Mon Jan 22 11:27:24 2018 -0500 +++ b/test-data/count/analyze_diff_expr/results.matrix Thu Jun 14 03:11:51 2018 -0400 @@ -1,14 +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 +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 +TR3788|c0_g1_i1 17.00 30.00 22.00 91.00 132.00 125.00 32.00 22.00 27.00 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 +TR3091|c0_g1_i1 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00 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 +TR4761|c0_g1_i1 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00 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 +TR5075|c0_g1_i1 13.00 22.00 21.00 6.00 8.00 10.00 163.00 121.00 142.00 +TR2672|c0_g1_i1 14.00 29.00 22.00 0.00 4.00 2.00 14.00 4.00 7.00 +TR4277|c0_g1_i1 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00 +TR127|c1_g1_i1 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 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
--- a/test-data/count/analyze_diff_expr/results.matrix.log2.centered.dat Mon Jan 22 11:27:24 2018 -0500 +++ b/test-data/count/analyze_diff_expr/results.matrix.log2.centered.dat Thu Jun 14 03:11:51 2018 -0400 @@ -1,14 +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 +TR3788|c0_g1_i1 -1.22775484082629 -0.443483531881724 -0.874117886211586 1.12588211378841 1.65760259323259 1.57960008123132 -0.353285722910146 -0.874117886211586 -0.590324920210995 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 +TR3091|c0_g1_i1 -2.42438780178849 -2.77802475640319 -2.62602166295814 1.02359379610527 1.32351327005887 1.20686835120661 1.43575453462855 1.4783149968566 1.36038927229391 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 +TR4761|c0_g1_i1 2.06406810079911 1.80544476674762 1.90822498634624 -1.67981690730689 -1.51400801433681 -1.59017969482221 -0.339510283104669 -0.357888812419525 -0.296334141902888 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 +TR5075|c0_g1_i1 -1.04544737992556 -0.329240345926152 -0.393370683345868 -2.04544737992556 -1.68287730054085 -1.39337068334587 2.50474970263492 2.07793503557972 2.30706903479522 +TR2672|c0_g1_i1 0.965440325233136 1.96544032523314 1.58211168568163 -2.94145027037538 -0.619522175488021 -1.35648776965423 0.965440325233136 -0.619522175488021 0.0585497296246169 +TR4277|c0_g1_i1 3.24415794782388 3.31812623217364 3.18414689752048 -1.98611482817144 -1.80411699442855 -1.51461037723356 -1.44630436384266 -1.5322044372483 -1.46308007659348 +TR127|c1_g1_i1 1.25755965737847 2.52059406321227 2.02309440374145 -0.479405936787734 -2.06436843750889 -1.06436843750889 -0.0643684375088904 -1.06436843750889 -1.06436843750889 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
--- a/test-data/count/analyze_diff_expr/results.matrix.log2.dat Mon Jan 22 11:27:24 2018 -0500 +++ b/test-data/count/analyze_diff_expr/results.matrix.log2.dat Thu Jun 14 03:11:51 2018 -0400 @@ -1,14 +0,0 @@ -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
--- a/test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor.dat Mon Jan 22 11:27:24 2018 -0500 +++ b/test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor.dat Thu Jun 14 03:11:51 2018 -0400 @@ -1,10 +0,0 @@ -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
--- a/test-data/count/contig_exn50_statistic/ExN50.stats Mon Jan 22 11:27:24 2018 -0500 +++ b/test-data/count/contig_exn50_statistic/ExN50.stats Thu Jun 14 03:11:51 2018 -0400 @@ -1,5 +1,4 @@ -#E min_expr E-N50 num_transcripts -E33 525311.050 541 1 -E67 525311.050 541 2 -E99 329523.810 380 3 -E100 0 279 7 +Ex ExN50 num_transcripts +33 541 1 +67 541 2 +100 279 7
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results Mon Jan 22 11:27:24 2018 -0500 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results Thu Jun 14 03:11:51 2018 -0400 @@ -1,38 +1,38 @@ sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj -TR4277|c0_g1_i1 wt_37 wt_GSNO 3852.97388871986 161.116814813422 2007.04535176664 4.57260002898197 0.121471586836965 37.6433711623376 0 0 -TR131|c0_g1_i1 wt_37 wt_GSNO 26.1866396538608 1340.30918254958 683.247911101723 -5.67373033438939 0.187375754459626 -30.2799599166492 2.10486694333775e-201 3.89400384517483e-200 -TR4761|c0_g1_i1 wt_37 wt_GSNO 1645.20640957447 193.196157329029 919.201283451752 3.08848040390227 0.143569117275296 21.5121501233448 1.19819880470067e-102 1.47777852579749e-101 -TR3091|c0_g1_i1 wt_37 wt_GSNO 16.7444693227929 328.569936894811 172.657203108802 -4.29037251456992 0.240582794801874 -17.8332474610379 3.90090325510546e-71 3.60833551097255e-70 -TR3638|c0_g1_i1 wt_37 wt_GSNO 583.00358519031 183.754416330029 383.37900076017 1.66018954854466 0.144513974558734 11.4880900176883 1.51422805973163e-30 1.12052876420141e-29 -TR2487|c0_g1_i1 wt_37 wt_GSNO 342.210853400436 920.407318992504 631.30908619647 -1.42691086642688 0.124648977132644 -11.4474334186348 2.42211055832184e-30 1.49363484429847e-29 -TR3788|c0_g1_i1 wt_37 wt_GSNO 19.5075441237117 134.95369713876 77.2306206312357 -2.77036684869735 0.263152237265066 -10.527620351967 6.4442989603998e-26 3.40627230763989e-25 -TR1479|c0_g1_i1 wt_37 wt_GSNO 129.593534475689 371.064629188207 250.329081831948 -1.51441062491813 0.145530800926874 -10.4061175728641 2.32511621828936e-25 1.07536625095883e-24 -TR2107|c1_g1_i1 wt_37 wt_GSNO 48.9228907410258 7.40521775805688 28.1640542495414 2.69488884014666 0.432209832999676 6.23514005094067 4.51374085119887e-10 1.85564901660398e-09 -TR3854|c0_g1_i1 wt_37 wt_GSNO 1573.69549271337 2374.56159860719 1974.12854566028 -0.593515573382884 0.111170659243154 -5.33877893163104 9.35746583039244e-08 3.4622623572452e-07 -TR2122|c0_g2_i2 wt_37 wt_GSNO 119.534640490118 199.143666337033 159.339153413576 -0.738644008220832 0.168659021315898 -4.37951081690053 1.18946017688789e-05 4.00091150407745e-05 -TR1449|c0_g1_i1 wt_37 wt_GSNO 180.814952011467 104.755290736358 142.785121373912 0.784193680180578 0.186004942516637 4.21598302480827 2.48692468039376e-05 7.49709472786912e-05 -TR4163|c0_g1_i1 wt_37 wt_GSNO 347.283468916919 232.772947466212 290.028208191566 0.576743600823335 0.13722219355458 4.20299068163444 2.63411436384591e-05 7.49709472786912e-05 -TR2672|c0_g1_i1 wt_37 wt_GSNO 18.3155337236093 2.26581902751323 10.2906763755613 2.88788179640237 0.725539563189254 3.98032298019437 6.88216980025882e-05 0.000181885916149697 -TR127|c1_g1_i1 wt_37 wt_GSNO 13.461799216177 1.21881296083961 7.34030608850831 3.33150202228086 0.915899815581865 3.63740877070095 0.000275394687501815 0.000667511143840185 -TR5055|c0_g2_i1 wt_37 wt_GSNO 23.3590211688541 5.52768338415684 14.4433522765055 2.04460941512382 0.563987307210913 3.62527558507482 0.000288653467606567 0.000667511143840185 -TR2844|c0_g1_i1 wt_37 wt_GSNO 158.206282615139 231.762548186068 194.984415400603 -0.550639207704626 0.154913717539885 -3.55448966333699 0.000378713397971402 0.000824258572055403 -TR5212|c0_g1_i1 wt_37 wt_GSNO 65.7079302129484 107.875371765755 86.7916509893515 -0.713874873222434 0.210087143945163 -3.39799408862815 0.000678818868686303 0.00139534989674407 -TR1894|c2_g1_i1 wt_37 wt_GSNO 13.3497721959996 2.96749216411516 8.15863218005739 2.04972102673103 0.716146945354672 2.86215146210796 0.00420775772107294 0.00819405450945783 -TR24|c0_g1_i1 wt_37 wt_GSNO 69.9065207344592 41.2394742844514 55.5729975094553 0.760351613917761 0.269735390145923 2.81887969356346 0.00481915767774413 0.00891544170382664 -TR2779|c0_g1_i1 wt_37 wt_GSNO 155.915506826481 205.619872596257 180.767689711369 -0.402350189521528 0.18910416680051 -2.12766432558821 0.0333649247395808 0.0587858197792614 -TR3807|c0_g1_i1 wt_37 wt_GSNO 3.48709246029019 0.350050334268211 1.9185713972792 2.6523001983829 1.38324824664578 1.91744338358239 0.055181627150862 0.092164962039527 -TR1492|c0_g1_i2 wt_37 wt_GSNO 1640.89375005483 1435.64893261411 1538.27134133447 0.192484568368337 0.101250195527162 1.90107848548993 0.057291733159706 0.092164962039527 -TR4084|c0_g1_i1 wt_37 wt_GSNO 93.2264707954139 121.352438036668 107.289454416041 -0.380198430346905 0.213412163689062 -1.78152183912463 0.0748272403991533 0.115358662282028 -TR1891|c0_g1_i1 wt_37 wt_GSNO 107.628573623499 135.399287466928 121.513930545214 -0.328810062058933 0.189329296532127 -1.73670989161013 0.0824383909023624 0.122008818535496 -TR4669|c0_g2_i1 wt_37 wt_GSNO 0 167.096667347181 83.5483336735905 -3.46077834317638 2.04233842282563 -1.69451757088734 0.0901669757000038 0.128314542342313 -TR1837|c2_g1_i1 wt_37 wt_GSNO 0.308903905435236 2.22601224010275 1.26745807276899 -2.41951712666755 1.51166579847997 -1.60056351681732 0.1094736282342 0.150019416469089 -TR5075|c0_g1_i1 wt_37 wt_GSNO 15.8633018853512 9.23822794034992 12.5507649128506 0.764028730403883 0.508108615055784 1.50367206491864 0.132665825459353 0.172493073735055 -TR4859|c0_g1_i1 wt_37 wt_GSNO 7.32690480813971 3.17910584569163 5.25300532691567 1.18248087647214 0.791530422232021 1.49391715499409 0.135197274008557 0.172493073735055 -TR939|c0_g1_i1 wt_37 wt_GSNO 84.2568220960088 96.9171174594069 90.5869697777078 -0.202690605185084 0.202556787736977 -1.00066064163834 0.316990901598642 0.384256032989688 -TR2278|c0_g1_i1 wt_37 wt_GSNO 486.5272515724 448.140178813055 467.333715192727 0.118822806572317 0.119966033346418 0.99047041281427 0.321944243856225 0.384256032989688 -TR2011|c5_g1_i1 wt_37 wt_GSNO 5.60408627995835 7.88255079488408 6.74331853742122 -0.48861876789566 0.691406970296359 -0.706702114510391 0.479751615248569 0.554712805131158 -TR2182|c3_g2_i6 wt_37 wt_GSNO 2.24974854180929 1.3031439398571 1.77644624083319 0.779605221657958 1.28583289420755 0.606303684693354 0.544313112275579 0.605163179078445 -TR3249|c0_g1_i1 wt_37 wt_GSNO 1.12573841927462 2.128954842887 1.62734663108081 -0.761341397480685 1.29336792501876 -0.58865028485196 0.556095894288301 0.605163179078445 -TR1678|c0_g1_i1 wt_37 wt_GSNO 0.595141051681226 0.700100668536423 0.647620860108824 -0.247288262290953 1.73789746083653 -0.14229162989393 0.886849657633351 0.935371730620685 -TR1122|c0_g1_i1 wt_37 wt_GSNO 1.41370386226057 1.3031439398571 1.35842390105883 0.162148276801819 1.43591594510694 0.112923237153511 0.910091413576882 0.935371730620685 -TR1982|c2_g1_i1 wt_37 wt_GSNO 5.73684100209948 5.71221669652109 5.72452884931028 -0.0101267142582557 0.715373046105777 -0.0141558510114153 0.988705642243408 0.988705642243408 +TR4277|c0_g1_i1 wt_37 wt_GSNO 3852.97388871986 161.116814813422 2007.04535176664 4.57661492404411 0.121615845393926 37.6317321909822 0 0 +TR131|c0_g1_i1 wt_37 wt_GSNO 26.1866396538608 1340.30918254958 683.247911101723 -5.68565819121436 0.188173369545147 -30.2149990987446 1.50487696827007e-200 2.48304699764561e-199 +TR4761|c0_g1_i1 wt_37 wt_GSNO 1645.20640957447 193.196157329029 919.201283451752 3.09227622940716 0.143766888218038 21.5089598706302 1.28350063536341e-102 1.41185069889975e-101 +TR3091|c0_g1_i1 wt_37 wt_GSNO 16.7444693227929 328.569936894811 172.657203108802 -4.30529554105297 0.242003292489129 -17.790235400398 8.41257542125902e-71 6.94037472253869e-70 +TR3638|c0_g1_i1 wt_37 wt_GSNO 583.00358519031 183.754416330029 383.37900076017 1.66225356244238 0.144704273829595 11.487245804501 1.5290952692426e-30 1.00920287770012e-29 +TR2487|c0_g1_i1 wt_37 wt_GSNO 342.210853400436 920.407318992504 631.30908619647 -1.42823125318501 0.124766100464837 -11.44727011475 2.42667678803784e-30 1.33467223342081e-29 +TR3788|c0_g1_i1 wt_37 wt_GSNO 19.5075441237117 134.95369713876 77.2306206312357 -2.78185518936858 0.26452057618315 -10.5165928091827 7.24461724546031e-26 3.41531955857415e-25 +TR1479|c0_g1_i1 wt_37 wt_GSNO 129.593534475689 371.064629188207 250.329081831948 -1.51632040995179 0.145721574162902 -10.405599985193 2.33778717307793e-25 9.64337208894648e-25 +TR2107|c1_g1_i1 wt_37 wt_GSNO 48.9228907410258 7.40521775805688 28.1640542495414 2.72565745131165 0.439033221898883 6.20831708252687 5.35550100392654e-10 1.96368370143973e-09 +TR3854|c0_g1_i1 wt_37 wt_GSNO 1573.69549271337 2374.56159860719 1974.12854566028 -0.593952181868433 0.11125243839418 -5.33877900063632 9.35746226940931e-08 3.08796254890507e-07 +TR2122|c0_g2_i2 wt_37 wt_GSNO 119.534640490118 199.143666337033 159.339153413576 -0.73989736621081 0.168946597067547 -4.37947481070002 1.18965671308434e-05 3.56897013925302e-05 +TR1449|c0_g1_i1 wt_37 wt_GSNO 180.814952011467 104.755290736358 142.785121373912 0.785811747593425 0.186397685526418 4.2157806057203 2.48915666101662e-05 6.6882655779165e-05 +TR4163|c0_g1_i1 wt_37 wt_GSNO 347.283468916919 232.772947466212 290.028208191566 0.5773903092812 0.137377906430929 4.20293425836637 2.63477128827014e-05 6.6882655779165e-05 +TR2672|c0_g1_i1 wt_37 wt_GSNO 18.3155337236093 2.26581902751323 10.2906763755613 2.9857084616452 0.761209385049731 3.92232218924907 8.76996107235725e-05 0.000206720510991278 +TR5055|c0_g2_i1 wt_37 wt_GSNO 23.3590211688541 5.52768338415684 14.4433522765055 2.08513896568298 0.577312677901881 3.61180179389265 0.00030407694239889 0.000668969273277559 +TR2844|c0_g1_i1 wt_37 wt_GSNO 158.206282615139 231.762548186068 194.984415400603 -0.551426184671915 0.155135532159318 -3.55448024702441 0.000378726959348647 0.000781124353656584 +TR127|c1_g1_i1 wt_37 wt_GSNO 13.461799216177 1.21881296083961 7.34030608850831 3.52517488060096 1.00261297574214 3.51598769005717 0.00043812129728732 0.000850470753557739 +TR5212|c0_g1_i1 wt_37 wt_GSNO 65.7079302129484 107.875371765755 86.7916509893515 -0.715754705745061 0.210644233010842 -3.39793164766215 0.000678973819799399 0.0012447853362989 +TR1894|c2_g1_i1 wt_37 wt_GSNO 13.3497721959996 2.96749216411516 8.15863218005739 2.116499695166 0.744618031030184 2.84239651333424 0.00447757649596373 0.00777684338772647 +TR24|c0_g1_i1 wt_37 wt_GSNO 69.9065207344592 41.2394742844514 55.5729975094553 0.763675526543044 0.270944643994893 2.81856660933825 0.00482386011442888 0.00795936918880766 +TR4669|c0_g2_i1 wt_37 wt_GSNO 0 167.096667347181 83.5483336735905 -10.0466852501689 3.90738405199054 -2.57120495873725 0.0101345328521317 0.0159256944819212 +TR2779|c0_g1_i1 wt_37 wt_GSNO 155.915506826481 205.619872596257 180.767689711369 -0.403209397282846 0.18950756245476 -2.12766916559914 0.033364523163095 0.0500467847446426 +TR3807|c0_g1_i1 wt_37 wt_GSNO 3.48709246029019 0.350050334268211 1.9185713972792 3.04810928058763 1.5874506366217 1.92012854464212 0.0548416645360559 0.0786858665082542 +TR1492|c0_g1_i2 wt_37 wt_GSNO 1640.89375005483 1435.64893261411 1538.27134133447 0.192601921423703 0.101311986688049 1.90107733270247 0.0572918841322824 0.0787763406818883 +TR4084|c0_g1_i1 wt_37 wt_GSNO 93.2264707954139 121.352438036668 107.289454416041 -0.381231151484282 0.21399248813321 -1.78151651401411 0.0748281095286258 0.0987731045777861 +TR1891|c0_g1_i1 wt_37 wt_GSNO 107.628573623499 135.399287466928 121.513930545214 -0.329513668205708 0.189733845104182 -1.7367152814764 0.0824374390602291 0.104632134191829 +TR1837|c2_g1_i1 wt_37 wt_GSNO 0.308903905435236 2.22601224010275 1.26745807276899 -2.87715913917267 1.7927876855897 -1.60485213184979 0.108526350064413 1 +TR5075|c0_g1_i1 wt_37 wt_GSNO 15.8633018853512 9.23822794034992 12.5507649128506 0.776103293030194 0.516446682273215 1.5027752518693 0.13289700980576 0.16070937436521 +TR4859|c0_g1_i1 wt_37 wt_GSNO 7.32690480813971 3.17910584569163 5.25300532691567 1.23041974278822 0.82607009598701 1.48948587869905 0.13635946915836 0.16070937436521 +TR939|c0_g1_i1 wt_37 wt_GSNO 84.2568220960088 96.9171174594069 90.5869697777078 -0.203187486812458 0.203052234052517 -1.00066609835923 0.316988262617008 0.354139456794138 +TR2278|c0_g1_i1 wt_37 wt_GSNO 486.5272515724 448.140178813055 467.333715192727 0.118924512672215 0.120068895863502 0.990468945491189 0.321944960721944 0.354139456794138 +TR2011|c5_g1_i1 wt_37 wt_GSNO 5.60408627995835 7.88255079488408 6.74331853742122 -0.50342873702063 0.712267625142964 -0.706797163383052 0.479692537619295 0.510640443272153 +TR2182|c3_g2_i6 wt_37 wt_GSNO 2.24974854180929 1.3031439398571 1.77644624083319 0.878491642458712 1.45214866443311 0.604959852923637 0.545205672528741 0.562243349795264 +TR3249|c0_g1_i1 wt_37 wt_GSNO 1.12573841927462 2.128954842887 1.62734663108081 -0.858277190977929 1.45820967054459 -0.588582841216099 0.556141147160533 1 +TR1678|c0_g1_i1 wt_37 wt_GSNO 0.595141051681226 0.700100668536423 0.647620860108824 -0.322353878735801 2.26929239960538 -0.142050393678601 0.887040200834538 1 +TR1122|c0_g1_i1 wt_37 wt_GSNO 1.41370386226057 1.3031439398571 1.35842390105883 0.189589394350501 1.67633508161709 0.113097552171736 0.909953215626095 1 +TR1982|c2_g1_i1 wt_37 wt_GSNO 5.73684100209948 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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.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset Thu Jun 14 03:11:51 2018 -0400 @@ -0,0 +1,7 @@ +sampleA sampleB 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 wt_37 wt_GSNO 3852.97388871986 161.116814813422 2007.04535176664 4.57260002898197 0.121471586836965 37.6433711623376 0 0 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00 +TR4761|c0_g1_i1 wt_37 wt_GSNO 1645.20640957447 193.196157329029 919.201283451752 3.08848040390227 0.143569117275296 21.5121501233448 1.19819880470067e-102 1.47777852579749e-101 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00 +TR2107|c1_g1_i1 wt_37 wt_GSNO 48.9228907410258 7.40521775805688 28.1640542495414 2.69488884014666 0.432209832999676 6.23514005094067 4.51374085119887e-10 1.85564901660398e-09 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00 +TR2672|c0_g1_i1 wt_37 wt_GSNO 18.3155337236093 2.26581902751323 10.2906763755613 2.88788179640237 0.725539563189254 3.98032298019437 6.88216980025882e-05 0.000181885916149697 14.00 29.00 22.00 0.00 4.00 2.00 14.00 4.00 7.00 +TR127|c1_g1_i1 wt_37 wt_GSNO 13.461799216177 1.21881296083961 7.34030608850831 3.33150202228086 0.915899815581865 3.63740877070095 0.000275394687501815 0.000667511143840185 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 +TR5055|c0_g2_i1 wt_37 wt_GSNO 23.3590211688541 5.52768338415684 14.4433522765055 2.04460941512382 0.563987307210913 3.62527558507482 0.000288653467606567 0.000667511143840185 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/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset Thu Jun 14 03:11:51 2018 -0400 @@ -0,0 +1,4 @@ +sampleA sampleB 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 wt_37 wt_GSNO 26.1866396538608 1340.30918254958 683.247911101723 -5.67373033438939 0.187375754459626 -30.2799599166492 2.10486694333775e-201 3.89400384517483e-200 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00 +TR3091|c0_g1_i1 wt_37 wt_GSNO 16.7444693227929 328.569936894811 172.657203108802 -4.29037251456992 0.240582794801874 -17.8332474610379 3.90090325510546e-71 3.60833551097255e-70 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00 +TR3788|c0_g1_i1 wt_37 wt_GSNO 19.5075441237117 134.95369713876 77.2306206312357 -2.77036684869735 0.263152237265066 -10.527620351967 6.4442989603998e-26 3.40627230763989e-25 17.00 30.00 22.00 91.00 132.00 125.00 32.00 22.00 27.00
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results Mon Jan 22 11:27:24 2018 -0500 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results Thu Jun 14 03:11:51 2018 -0400 @@ -1,39 +1,38 @@ -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 +sampleA sampleB logFC logCPM PValue FDR +TR131|c0_g1_i1 wt_37 wt_GSNO -5.83641794955382 16.0393491449056 0 0 +TR4277|c0_g1_i1 wt_37 wt_GSNO 4.41329536892161 17.453649857324 0 0 +TR3091|c0_g1_i1 wt_37 wt_GSNO -4.45192710783926 14.0403115023365 4.66239713643175e-192 5.75028980159916e-191 +TR4761|c0_g1_i1 wt_37 wt_GSNO 2.92754337500687 16.3361488759619 3.05265683396309e-191 2.82370757141586e-190 +TR2487|c0_g1_i1 wt_37 wt_GSNO -1.58705168340508 15.8893887856701 9.57106937146597e-124 7.08259133488482e-123 +TR1479|c0_g1_i1 wt_37 wt_GSNO -1.67065982572176 14.5610246448295 4.39649357092684e-84 2.71117103540489e-83 +TR3638|c0_g1_i1 wt_37 wt_GSNO 1.49937182627392 15.1071990563814 1.60652562072048e-64 8.49163542380826e-64 +TR3854|c0_g1_i1 wt_37 wt_GSNO -0.756864683109858 17.5153338325952 9.14141417630157e-40 4.22790405653948e-39 +TR2122|c0_g2_i2 wt_37 wt_GSNO -0.90394318029981 13.8984589155106 3.98287653266084e-13 1.63740479676057e-12 +TR2844|c0_g1_i1 wt_37 wt_GSNO -0.707834005847516 14.1849675326065 1.90004997002049e-12 7.0301848890758e-12 +TR3788|c0_g1_i1 wt_37 wt_GSNO -2.92402824575823 12.8707284018497 1.35908019280542e-09 4.57145155761824e-09 +TR4669|c0_g2_i1 wt_37 wt_GSNO -10.5373989771184 13.0207784411552 2.87822490296537e-08 8.87452678414323e-08 +TR2672|c0_g1_i1 wt_37 wt_GSNO 2.77705541360002 10.2430402179839 7.41806563943484e-08 2.11129560506992e-07 +TR4163|c0_g1_i1 wt_37 wt_GSNO 0.420123134789911 14.7306522277754 2.74345107938324e-06 7.25054928122714e-06 +TR127|c1_g1_i1 wt_37 wt_GSNO 3.26487561187968 9.85808314705506 6.1191913603037e-06 1.50940053554158e-05 +TR2107|c1_g1_i1 wt_37 wt_GSNO 2.54741701164587 11.489948731934 1.24782096095324e-05 2.88558597220436e-05 +TR2779|c0_g1_i1 wt_37 wt_GSNO -0.571512278204146 14.0677635717422 7.39487278515011e-05 0.000160947231206208 +TR1894|c2_g1_i1 wt_37 wt_GSNO 1.88989717290856 9.93884262525918 0.00064827406279645 0.00133256335130381 +TR5055|c0_g2_i1 wt_37 wt_GSNO 1.89504810994952 10.6064804346292 0.00584438080176016 0.011381162613954 +TR3807|c0_g1_i1 wt_37 wt_GSNO 2.66606066906632 8.56455983886691 0.0188051214716541 0.0347894747225602 +TR5212|c0_g1_i1 wt_37 wt_GSNO -0.867441722907523 13.0312878134755 0.0313380642877521 0.055214684697468 +TR1449|c0_g1_i1 wt_37 wt_GSNO 0.636828244112651 13.716963541734 0.0836258106887223 0.140643408885578 +TR1837|c2_g1_i1 wt_37 wt_GSNO -2.70136949048315 8.19724487849862 0.11443273811818 0.184087448277072 +TR4859|c0_g1_i1 wt_37 wt_GSNO 1.06021338602227 9.44252758756623 0.17021260004507 0.262411091736149 +TR4084|c0_g1_i1 wt_37 wt_GSNO -0.527027354857722 13.3333941866224 0.195100037539558 0.280916147575458 +TR1891|c0_g1_i1 wt_37 wt_GSNO -0.481344817930584 13.5015018099629 0.197400536134106 0.280916147575458 +TR24|c0_g1_i1 wt_37 wt_GSNO 0.590686928315332 12.3882336221811 0.209814398393357 0.287523434835341 +TR2011|c5_g1_i1 wt_37 wt_GSNO -0.668008806764204 9.63014074618193 0.239244885423374 0.316145027166602 +TR939|c0_g1_i1 wt_37 wt_GSNO -0.361607139894815 13.0833886152319 0.340252678428006 0.434115486270215 +TR5075|c0_g1_i1 wt_37 wt_GSNO 0.617585416067661 10.4358029661318 0.377913209145196 0.466092957945741 +TR1492|c0_g1_i2 wt_37 wt_GSNO 0.0311900896664335 17.1368189470585 0.559289231968699 0.657620159615942 +TR3249|c0_g1_i1 wt_37 wt_GSNO -0.894241538356016 8.33957569586088 0.568752570478653 0.657620159615942 +TR2278|c0_g1_i1 wt_37 wt_GSNO -0.0373200220187202 15.4258149088647 0.636489077475997 0.713639268685208 +TR2182|c3_g2_i6 wt_37 wt_GSNO 0.714549920613349 8.45775163335771 0.790296098133788 0.860028106792652 +TR1982|c2_g1_i1 wt_37 wt_GSNO -0.181275971858276 9.49467590956657 0.873422282667325 0.923332127391172 +TR1678|c0_g1_i1 wt_37 wt_GSNO -0.476606391142577 7.93769527756871 1 1 +TR1122|c0_g1_i1 wt_37 wt_GSNO 0.0647357997613641 8.26206759454538 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
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results Mon Jan 22 11:27:24 2018 -0500 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results Thu Jun 14 03:11:51 2018 -0400 @@ -1,39 +1,38 @@ -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 +sampleA sampleB logFC logCPM PValue FDR +TR131|c0_g1_i1 wt_37 wt_GSNO -5.82360148900389 16.1142242655408 6.54502972918692e-10 2.42166099979916e-08 +TR4277|c0_g1_i1 wt_37 wt_GSNO 4.41183386172098 17.3836256000268 1.7102544921365e-09 3.16397081045253e-08 +TR3091|c0_g1_i1 wt_37 wt_GSNO -4.43700179801176 14.1203688767724 4.42033048679943e-08 5.45174093371929e-07 +TR2487|c0_g1_i1 wt_37 wt_GSNO -1.58598083708684 15.9280757073272 7.01720228399608e-08 6.49091211269637e-07 +TR4761|c0_g1_i1 wt_37 wt_GSNO 2.92043321768346 16.2716301848411 5.72725934421127e-07 4.23817191471634e-06 +TR1479|c0_g1_i1 wt_37 wt_GSNO -1.67738254434993 14.6016057367881 1.03919750932427e-06 5.8615543150164e-06 +TR3638|c0_g1_i1 wt_37 wt_GSNO 1.50288215872986 15.0600281889274 1.12469315856867e-06 5.8615543150164e-06 +TR3788|c0_g1_i1 wt_37 wt_GSNO -2.93907650045598 12.9393872783943 2.35975448958169e-06 9.70121290161359e-06 +TR3854|c0_g1_i1 wt_37 wt_GSNO -0.759397690410038 17.5353083640786 1.26736309513868e-06 5.8615543150164e-06 +TR2107|c1_g1_i1 wt_37 wt_GSNO 2.46233758474327 11.260249244859 0.000163907571391062 0.000551325467406299 +TR2122|c0_g2_i2 wt_37 wt_GSNO -0.898543060702643 13.9151768182402 0.000124408949544541 0.000460313113314803 +TR2844|c0_g1_i1 wt_37 wt_GSNO -0.712202725875737 14.1973066750225 0.000243984033514546 0.000752284103336518 +TR5212|c0_g1_i1 wt_37 wt_GSNO -0.87701850957337 13.0391017777502 0.000473838954429694 0.00134861856260759 +TR4163|c0_g1_i1 wt_37 wt_GSNO 0.417694804483349 14.7107025605232 0.000805848497363634 0.00212974245731817 +TR2672|c0_g1_i1 wt_37 wt_GSNO 2.90562993555483 9.81450205355949 0.00822748279906008 0.0169120479758457 +TR1449|c0_g1_i1 wt_37 wt_GSNO 0.640011354440497 13.6755402195434 0.00227354555819909 0.00560807904355776 +TR127|c1_g1_i1 wt_37 wt_GSNO 3.09466453837236 9.33233275488244 0.00997545255499303 0.0184545872267371 +TR1894|c2_g1_i1 wt_37 wt_GSNO 1.8273232048322 9.47625819175118 0.0170307015491222 0.0286425435144327 +TR5055|c0_g2_i1 wt_37 wt_GSNO 1.79897959483123 10.2910629958573 0.0144290410083875 0.025422596062397 +TR939|c0_g1_i1 wt_37 wt_GSNO -0.363394684962815 13.0708604932728 0.00579686595094712 0.0134052525115652 +TR1837|c2_g1_i1 wt_37 wt_GSNO -2.21418127698954 7.02378849272624 0.0306005987832276 0.0471759231241425 +TR1891|c0_g1_i1 wt_37 wt_GSNO -0.477062796219233 13.500309435849 0.00675073796972544 0.0146927826399907 +TR3807|c0_g1_i1 wt_37 wt_GSNO 1.91879773659378 7.35599058475032 0.0402625583382777 0.0572967176352414 +TR2779|c0_g1_i1 wt_37 wt_GSNO -0.600036558858359 14.0748557225205 0.00991998269314111 0.0184545872267371 +TR24|c0_g1_i1 wt_37 wt_GSNO 0.588796779058576 12.310400953631 0.0185008090691583 0.0297621711112546 +TR4859|c0_g1_i1 wt_37 wt_GSNO 1.06036244689068 8.9138577436531 0.104550838513832 0.143273371296733 +TR4084|c0_g1_i1 wt_37 wt_GSNO -0.567278869966665 13.330468891507 0.0372234219214301 0.0550906644437166 +TR2011|c5_g1_i1 wt_37 wt_GSNO -0.789577978066661 9.33004998835934 0.161975973261362 0.206659000367944 +TR2182|c3_g2_i6 wt_37 wt_GSNO 1.02218394394404 7.37517597546907 0.329234058043314 0.406055338253421 +TR5075|c0_g1_i1 wt_37 wt_GSNO 0.549449880041588 10.1791103984097 0.127566698813275 0.168570280574684 +TR4669|c0_g2_i1 wt_37 wt_GSNO -6.27345157840298 13.126293325041 0.423017017822531 0.489113426857301 +TR1678|c0_g1_i1 wt_37 wt_GSNO -0.330222398445961 5.95523974949609 0.735881722270124 0.79829094077818 +TR1122|c0_g1_i1 wt_37 wt_GSNO 0.193564460109425 7.01613737702005 0.875819231521416 0.875819231521416 +TR3249|c0_g1_i1 wt_37 wt_GSNO -0.276543877903423 7.32180296800742 0.776715509946338 0.79829094077818 +TR1982|c2_g1_i1 wt_37 wt_GSNO -0.131251756802268 9.08566155151058 0.763275890632561 0.79829094077818 +TR2278|c0_g1_i1 wt_37 wt_GSNO -0.0407242590322052 15.424279874284 0.616230913043451 0.69092556916993 +TR1492|c0_g1_i2 wt_37 wt_GSNO 0.0323916193661019 17.1363857315734 0.39613877470297 0.472810795613223
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf has changed
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results Mon Jan 22 11:27:24 2018 -0500 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results Thu Jun 14 03:11:51 2018 -0400 @@ -1,39 +1,39 @@ sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj -TR4277|c0_g1_i1 wt_37 wt_ph8 4705.34614971641 162.902721493704 2434.12443560506 4.84804012036106 0.130783542648097 37.0691909868646 8.81406568413535e-301 3.34934495997143e-299 -TR131|c0_g1_i1 wt_37 wt_ph8 32.0461070493257 1436.30905989883 734.177583474076 -5.48335951236111 0.197548955320184 -27.7569653733364 1.43583336471356e-169 2.72808339295576e-168 -TR3091|c0_g1_i1 wt_37 wt_ph8 20.4914097091341 321.651020117047 171.071214913091 -3.97084930318667 0.245881056057371 -16.1494722971263 1.14537343838751e-58 1.45080635529084e-57 -TR4761|c0_g1_i1 wt_37 wt_ph8 2012.6141923276 384.620292965437 1198.61724264652 2.38432084623308 0.148099583891604 16.0994432501458 2.57410332221217e-58 2.44539815610156e-57 -TR5075|c0_g1_i1 wt_37 wt_ph8 19.3833722195684 136.98672801182 78.1850501156942 -2.80247674171473 0.269715041166808 -10.3905096637956 2.73885623424733e-25 2.08153073802797e-24 -TR2779|c0_g1_i1 wt_37 wt_ph8 191.51955185349 1058.15934185376 624.839446853626 -2.45909834872711 0.247058756007882 -9.95349603658112 2.43476309780354e-23 1.54201662860891e-22 -TR1891|c0_g1_i1 wt_37 wt_ph8 131.416087212132 376.595292171713 254.005689691923 -1.51504907455703 0.163541333568612 -9.26401320997792 1.96889433896152e-20 1.06882835543625e-19 -TR1492|c0_g1_i2 wt_37 wt_ph8 2006.11782336441 890.823502721036 1448.47066304272 1.17018000582475 0.127273970398445 9.19418167093695 3.77859650812701e-20 1.79483334136033e-19 -TR2487|c0_g1_i1 wt_37 wt_ph8 418.818667162757 965.862817209246 692.340742186001 -1.2054117169244 0.138501088570193 -8.70326529104133 3.22468912161225e-18 1.36153540690295e-17 -TR3638|c0_g1_i1 wt_37 wt_ph8 713.131183384274 326.063958913919 519.597571149096 1.12815426477841 0.141332330235517 7.98228022490288 1.43654437320665e-15 5.45886861818526e-15 -TR2107|c1_g1_i1 wt_37 wt_ph8 59.5986596731862 1.89840873462066 30.7485342039034 4.82151434610286 0.613172060454942 7.86323229164347 3.74345886500564e-15 1.29319488063831e-14 -TR2122|c0_g2_i2 wt_37 wt_ph8 146.135958637131 360.821667264163 253.478812950647 -1.30371385707787 0.169650604759161 -7.68469914344628 1.53356953387865e-14 4.85630352394907e-14 -TR1479|c0_g1_i1 wt_37 wt_ph8 158.005105094407 334.827472148091 246.416288621249 -1.0787542477693 0.165556938369539 -6.51591083039607 7.22498877976404e-11 2.1119197971618e-10 -TR24|c0_g1_i1 wt_37 wt_ph8 85.6614643869141 199.923709280262 142.792586833588 -1.2279226670979 0.196562275775691 -6.24699048814003 4.18436531652641e-10 1.13575630020003e-09 -TR4163|c0_g1_i1 wt_37 wt_ph8 424.593720981574 227.471218917767 326.03246994967 0.900981410818221 0.155876696706134 5.78009048085484 7.46604610022994e-09 1.89139834539158e-08 -TR1449|c0_g1_i1 wt_37 wt_ph8 220.782434528097 117.26089394399 169.021664236043 0.914395516820343 0.174920034977504 5.22750591113215 1.71811907274331e-07 4.08053279776536e-07 -TR2278|c0_g1_i1 wt_37 wt_ph8 594.657329919233 348.341653317169 471.499491618201 0.772496794598277 0.157892732036131 4.89254182023719 9.95419556957436e-07 2.2250554802578e-06 -TR5055|c0_g2_i1 wt_37 wt_ph8 28.6665933385886 6.05959103586122 17.3630921872249 2.18372312866756 0.505600668447204 4.31906693354301 1.5669025864333e-05 3.30790546024808e-05 -TR127|c1_g1_i1 wt_37 wt_ph8 16.3791628279609 1.58772512712498 8.98344397754296 3.22742307122337 0.758365755070441 4.25576056097574 2.08339575851481e-05 4.16679151702962e-05 -TR1894|c2_g1_i1 wt_37 wt_ph8 16.2826445742552 1.67571344127509 8.97917900776516 3.18830464179373 0.7590595028564 4.20033558607184 2.66519649541344e-05 5.06387334128554e-05 -TR2672|c0_g1_i1 wt_37 wt_ph8 22.3129914439134 7.89947501226409 15.1062332280887 1.46563545973546 0.482353842293509 3.0385068620302 0.00237753690029721 0.00429545997952877 -TR4859|c0_g1_i1 wt_37 wt_ph8 8.91205730249659 1.28188505334354 5.09697117792006 2.65126611500267 0.876469721997014 3.02493748325022 0.00248684525130613 0.00429545997952877 -TR1678|c0_g1_i1 wt_37 wt_ph8 0.738899982352077 7.85275634721875 4.29582816478541 -3.18849648433777 1.0594001628342 -3.00971870327794 0.00261489744098202 0.00432026533727463 -TR4084|c0_g1_i1 wt_37 wt_ph8 113.2594381118 173.837287636503 143.548362874151 -0.608939120027998 0.203268581921877 -2.99573654851409 0.00273782859610482 0.00433489527716597 -TR3807|c0_g1_i1 wt_37 wt_ph8 4.23896204531587 0.352255997713617 2.29560902151474 3.15525660545126 1.31164110647326 2.4055792319098 0.0161468501576278 0.0245432122395943 -TR3249|c0_g1_i1 wt_37 wt_ph8 1.36481976577862 4.37661229401476 2.87071602989669 -1.55893212196469 1.01682768784581 -1.53313303777885 0.125243078950272 0.176625758092245 -TR1859|c3_g1_i1 wt_37 wt_ph8 0.361569353912422 2.25550826604853 1.30853880998047 -2.19284922770108 1.43126836745787 -1.53210206943641 0.125497249170806 0.176625758092245 -TR2090|c0_g1_i1 wt_37 wt_ph8 0 5.87877087384675 2.93938543692337 -2.86225136793822 1.9729684338102 -1.45073348305458 0.146854088052773 0.19930197664305 -TR1982|c2_g1_i1 wt_37 wt_ph8 7.00144976454503 11.520013112092 9.26073143831853 -0.712688609925078 0.555640746749963 -1.28264281209345 0.199617243880331 0.261567423015607 -TR1837|c2_g1_i1 wt_37 wt_ph8 0.377330628439655 1.67813520813222 1.02773291828594 -1.7572235261621 1.52690431775837 -1.15084062945205 0.249797806431129 0.316410554812763 -TR5212|c0_g1_i1 wt_37 wt_ph8 80.2050001877881 94.8352723753388 87.5201362815635 -0.23592411895009 0.215502649097795 -1.09476203628025 0.273620902411289 0.335406267471903 -TR3854|c0_g1_i1 wt_37 wt_ph8 1925.26464813324 2107.16376011081 2016.21420412203 -0.130483054839334 0.130739272627028 -0.998040238540833 0.318259846991125 0.377933568301961 -TR1122|c0_g1_i1 wt_37 wt_ph8 1.69354093201913 0.660517838352177 1.17702938518565 1.18649040337028 1.40558655511286 0.84412475279761 0.398599697111289 0.448776409473292 -TR2844|c0_g1_i1 wt_37 wt_ph8 193.030766468894 213.82243412349 203.426600296192 -0.143791883173722 0.17140940841448 -0.838879758723761 0.401536787423471 0.448776409473292 -TR2011|c5_g1_i1 wt_37 wt_ph8 6.84875389533898 4.81927837273561 5.8340161340373 0.467659672901774 0.714270969980296 0.654737057162879 0.512637061952329 0.556577381548243 -TR2182|c3_g2_i6 wt_37 wt_ph8 2.76248771922916 1.94482465855284 2.353656188891 0.479324872360299 1.02378035563408 0.468191120998245 0.639647921157653 0.675183916777523 -TR3788|c0_g1_i1 wt_37 wt_ph8 23.7579432209456 26.0024682525169 24.8802057367313 -0.124358222905796 0.350105186670918 -0.355202458119214 0.72243792333433 0.741963272613636 -TR939|c0_g1_i1 wt_37 wt_ph8 103.002135647151 102.820214322362 102.911174984756 0.000971215955472081 0.195414642848595 0.00497002651037041 0.996034508905975 0.996034508905975 +TR4277|c0_g1_i1 wt_37 wt_ph8 4705.34614971641 162.902721493704 2434.12443560506 4.85332629705957 0.130960775627329 37.0593887659196 1.26787233139066e-300 4.81791485928452e-299 +TR131|c0_g1_i1 wt_37 wt_ph8 32.0461070493257 1436.30905989883 734.177583474076 -5.49708942597102 0.198466854292743 -27.6977707212645 7.42748041559505e-169 1.41122127896306e-167 +TR3091|c0_g1_i1 wt_37 wt_ph8 20.4914097091341 321.651020117047 171.071214913091 -3.98630633515117 0.247421953542878 -16.1113687693051 2.12272588309166e-58 2.47056970916163e-57 +TR4761|c0_g1_i1 wt_37 wt_ph8 2012.6141923276 384.620292965437 1198.61724264652 2.3876556238738 0.148312557773369 16.0988095662291 2.60059969385434e-58 2.47056970916163e-57 +TR5075|c0_g1_i1 wt_37 wt_ph8 19.3833722195684 136.98672801182 78.1850501156942 -2.81556781738656 0.271397918695418 -10.3743161735385 3.24527446090745e-25 2.46640859028966e-24 +TR2779|c0_g1_i1 wt_37 wt_ph8 191.51955185349 1058.15934185376 624.839446853626 -2.46872482043468 0.248047686960726 -9.95262181511717 2.45625242439133e-23 1.55562653544784e-22 +TR1891|c0_g1_i1 wt_37 wt_ph8 131.416087212132 376.595292171713 254.005689691923 -1.51763504949468 0.1638333296262 -9.26328637132193 1.98234808919548e-20 1.07613181984897e-19 +TR1492|c0_g1_i2 wt_37 wt_ph8 2006.11782336441 890.823502721036 1448.47066304272 1.17138763330801 0.12740597231583 9.19413440371721 3.78025797563847e-20 1.79562253842827e-19 +TR2487|c0_g1_i1 wt_37 wt_ph8 418.818667162757 965.862817209246 692.340742186001 -1.2068861494209 0.138672539999103 -8.70313725722989 3.22833072204789e-18 1.36307297153133e-17 +TR3638|c0_g1_i1 wt_37 wt_ph8 713.131183384274 326.063958913919 519.597571149096 1.12959116050602 0.141514345090045 7.98216717737888 1.43786102301427e-15 5.46387188745423e-15 +TR2122|c0_g2_i2 wt_37 wt_ph8 146.135958637131 360.821667264163 253.478812950647 -1.30611123021679 0.169971549866392 -7.68429323168187 1.53843927144304e-14 5.31460839225778e-14 +TR2107|c1_g1_i1 wt_37 wt_ph8 59.5986596731862 1.89840873462066 30.7485342039034 4.94663101068376 0.648801734442531 7.62425676148051 2.45444399373987e-14 7.77240598017624e-14 +TR1479|c0_g1_i1 wt_37 wt_ph8 158.005105094407 334.827472148091 246.416288621249 -1.08064044509537 0.1658526880096 -6.5156643408325 7.23686413447617e-11 2.11539105469303e-10 +TR24|c0_g1_i1 wt_37 wt_ph8 85.6614643869141 199.923709280262 142.792586833588 -1.2309601921531 0.197065470330035 -6.24645296860761 4.19878369504606e-10 1.13966986008393e-09 +TR4163|c0_g1_i1 wt_37 wt_ph8 424.593720981574 227.471218917767 326.03246994967 0.902378343080323 0.156120482680011 5.78001251078543 7.46950706226027e-09 1.89227512243927e-08 +TR1449|c0_g1_i1 wt_37 wt_ph8 220.782434528097 117.26089394399 169.021664236043 0.916182468982544 0.175267159439457 5.22734819182726 1.71958482582468e-07 4.0840139613336e-07 +TR2278|c0_g1_i1 wt_37 wt_ph8 594.657329919233 348.341653317169 471.499491618201 0.77372548280461 0.158144801146882 4.8925129197639 9.95565784679233e-07 2.22538234222417e-06 +TR5055|c0_g2_i1 wt_37 wt_ph8 28.6665933385886 6.05959103586122 17.3630921872249 2.22056293047175 0.515653625436263 4.30630722045843 1.66002467176804e-05 3.50449652928809e-05 +TR127|c1_g1_i1 wt_37 wt_ph8 16.3791628279609 1.58772512712498 8.98344397754296 3.35782864860774 0.805715621214412 4.16751091848842 3.07943766984562e-05 6.15887533969124e-05 +TR1894|c2_g1_i1 wt_37 wt_ph8 16.2826445742552 1.67571344127509 8.97917900776516 3.31835899440704 0.806156235895963 4.1162728099709 3.85048512190331e-05 7.31592173161629e-05 +TR2672|c0_g1_i1 wt_37 wt_ph8 22.3129914439134 7.89947501226409 15.1062332280887 1.4879160019133 0.490304786216723 3.03467566244728 0.00240794483755529 0.00435723351557623 +TR4084|c0_g1_i1 wt_37 wt_ph8 113.2594381118 173.837287636503 143.548362874151 -0.610546095515356 0.203809508378262 -2.99567032163292 0.00273842322103228 0.00473000374541939 +TR4859|c0_g1_i1 wt_37 wt_ph8 8.91205730249659 1.28188505334354 5.09697117792006 2.79846628921536 0.943303749490582 2.96666507551426 0.00301048704228202 0.00497384815681378 +TR1678|c0_g1_i1 wt_37 wt_ph8 0.738899982352077 7.85275634721875 4.29582816478541 -3.47431884008145 1.21198503063676 -2.8666351087324 0.00414861034620894 0.00656863304816415 +TR3807|c0_g1_i1 wt_37 wt_ph8 4.23896204531587 0.352255997713617 2.29560902151474 3.60257127355045 1.494771199452 2.41011552461754 0.0159474699414718 0.0242401543110371 +TR1859|c3_g1_i1 wt_37 wt_ph8 0.361569353912422 2.25550826604853 1.30853880998047 -2.58650633406891 1.68391965639604 -1.53600340980911 0.124537544060973 0.181135380859875 +TR3249|c0_g1_i1 wt_37 wt_ph8 1.36481976577862 4.37661229401476 2.87071602989669 -1.67837058189371 1.10474169040967 -1.51924254915312 0.12870145482149 0.181135380859875 +TR2090|c0_g1_i1 wt_37 wt_ph8 0 5.87877087384675 2.93938543692337 -4.93100736412614 3.57047444665656 -1.38105101655149 0.167263275059569 0.227000159009415 +TR1982|c2_g1_i1 wt_37 wt_ph8 7.00144976454503 11.520013112092 9.26073143831853 -0.727260398375603 0.567300823658434 -1.28196605406919 0.199854554547715 0.261878381821143 +TR1837|c2_g1_i1 wt_37 wt_ph8 0.377330628439655 1.67813520813222 1.02773291828594 -2.14007669057536 1.85335822648042 -1.15470212935543 0.248212427250959 0.314402407851215 +TR5212|c0_g1_i1 wt_37 wt_ph8 80.2050001877881 94.8352723753388 87.5201362815635 -0.236625075567938 0.21614403033503 -1.09475646956875 0.273623341840838 0.335409257740381 +TR3854|c0_g1_i1 wt_37 wt_ph8 1925.26464813324 2107.16376011081 2016.21420412203 -0.130625245556183 0.13088163358419 -0.998041069468758 0.318259444082768 0.377933089848287 +TR2844|c0_g1_i1 wt_37 wt_ph8 193.030766468894 213.82243412349 203.426600296192 -0.144061748535941 0.17173092225162 -0.838880654963596 0.401536284440308 0.450271927171228 +TR1122|c0_g1_i1 wt_37 wt_ph8 1.69354093201913 0.660517838352177 1.17702938518565 1.3946217378633 1.66721495733336 0.836497856337578 0.402874882205836 0.450271927171228 +TR2011|c5_g1_i1 wt_37 wt_ph8 6.84875389533898 4.81927837273561 5.8340161340373 0.48395696149425 0.739237535887472 0.654670438120067 0.512679962329315 0.556623959100399 +TR2182|c3_g2_i6 wt_37 wt_ph8 2.76248771922916 1.94482465855284 2.353656188891 0.516404389322083 1.10366040723297 0.467901526536393 0.63985501178297 0.675402512437579 +TR3788|c0_g1_i1 wt_37 wt_ph8 23.7579432209456 26.0024682525169 24.8802057367313 -0.125340757750783 0.352879389384874 -0.355194328490741 0.722444013290729 0.741969527163451 +TR939|c0_g1_i1 wt_37 wt_ph8 103.002135647151 102.820214322362 102.911174984756 0.000973457550309434 0.195891269167835 0.00496937691222674 0.996035027203904 0.996035027203904
--- /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.P0.001_C2.wt_37-UP.subset Thu Jun 14 03:11:51 2018 -0400 @@ -0,0 +1,7 @@ +sampleA sampleB 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 wt_37 wt_ph8 4705.34614971641 162.902721493704 2434.12443560506 4.84804012036106 0.130783542648097 37.0691909868646 8.81406568413535e-301 3.34934495997143e-299 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00 +TR4761|c0_g1_i1 wt_37 wt_ph8 2012.6141923276 384.620292965437 1198.61724264652 2.38432084623308 0.148099583891604 16.0994432501458 2.57410332221217e-58 2.44539815610156e-57 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00 +TR2107|c1_g1_i1 wt_37 wt_ph8 59.5986596731862 1.89840873462066 30.7485342039034 4.82151434610286 0.613172060454942 7.86323229164347 3.74345886500564e-15 1.29319488063831e-14 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00 +TR5055|c0_g2_i1 wt_37 wt_ph8 28.6665933385886 6.05959103586122 17.3630921872249 2.18372312866756 0.505600668447204 4.31906693354301 1.5669025864333e-05 3.30790546024808e-05 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00 +TR127|c1_g1_i1 wt_37 wt_ph8 16.3791628279609 1.58772512712498 8.98344397754296 3.22742307122337 0.758365755070441 4.25576056097574 2.08339575851481e-05 4.16679151702962e-05 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 +TR1894|c2_g1_i1 wt_37 wt_ph8 16.2826445742552 1.67571344127509 8.97917900776516 3.18830464179373 0.7590595028564 4.20033558607184 2.66519649541344e-05 5.06387334128554e-05 21.00 14.00 11.00 1.00 2.00 5.00 1.00 3.00 1.00
--- /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.P0.001_C2.wt_ph8-UP.subset Thu Jun 14 03:11:51 2018 -0400 @@ -0,0 +1,5 @@ +sampleA sampleB 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 wt_37 wt_ph8 32.0461070493257 1436.30905989883 734.177583474076 -5.48335951236111 0.197548955320184 -27.7569653733364 1.43583336471356e-169 2.72808339295576e-168 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00 +TR3091|c0_g1_i1 wt_37 wt_ph8 20.4914097091341 321.651020117047 171.071214913091 -3.97084930318667 0.245881056057371 -16.1494722971263 1.14537343838751e-58 1.45080635529084e-57 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00 +TR5075|c0_g1_i1 wt_37 wt_ph8 19.3833722195684 136.98672801182 78.1850501156942 -2.80247674171473 0.269715041166808 -10.3905096637956 2.73885623424733e-25 2.08153073802797e-24 13.00 22.00 21.00 6.00 8.00 10.00 163.00 121.00 142.00 +TR2779|c0_g1_i1 wt_37 wt_ph8 191.51955185349 1058.15934185376 624.839446853626 -2.45909834872711 0.247058756007882 -9.95349603658112 2.43476309780354e-23 1.54201662860891e-22 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results Mon Jan 22 11:27:24 2018 -0500 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results Thu Jun 14 03:11:51 2018 -0400 @@ -1,39 +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 +sampleA sampleB logFC logCPM PValue FDR +TR131|c0_g1_i1 wt_37 wt_ph8 -5.83867709149149 16.0447742820606 3.67956255674e-64 1.3982337715612e-62 +TR3091|c0_g1_i1 wt_37 wt_ph8 -4.35104356420213 13.9337836495047 7.47918124727105e-59 1.4210444369815e-57 +TR4277|c0_g1_i1 wt_37 wt_ph8 4.51249642920563 17.4585638169146 1.30305812944242e-53 1.65054029729373e-52 +TR5075|c0_g1_i1 wt_37 wt_ph8 -3.18286810352713 12.8084040893566 8.25600206225396e-24 7.84320195914126e-23 +TR2107|c1_g1_i1 wt_37 wt_ph8 4.48477961203985 11.2510359028096 1.80754966502889e-22 1.37373774542196e-21 +TR2779|c0_g1_i1 wt_37 wt_ph8 -2.75442228103487 15.7797198210508 8.23352696880425e-15 5.21456708024269e-14 +TR1891|c0_g1_i1 wt_37 wt_ph8 -1.85607282303223 14.4424161372431 4.82341414399837e-12 2.61842482102769e-11 +TR4761|c0_g1_i1 wt_37 wt_ph8 2.05815692521639 16.4916266891202 6.53530817860542e-12 3.10427138483757e-11 +TR1479|c0_g1_i1 wt_37 wt_ph8 -1.43256512308186 14.3771181295432 1.13197856555697e-09 4.77946505457389e-09 +TR2122|c0_g2_i2 wt_37 wt_ph8 -1.63807722824331 14.4300672231344 2.54380104198531e-09 9.66644395954419e-09 +TR24|c0_g1_i1 wt_37 wt_ph8 -1.56169455062581 13.613754007054 1.01137959952142e-08 3.49385679834671e-08 +TR2487|c0_g1_i1 wt_37 wt_ph8 -1.52157644373511 15.8810635663776 2.37540305111961e-07 7.52210966187877e-07 +TR4084|c0_g1_i1 wt_37 wt_ph8 -0.991060679215133 13.5661427311877 4.21767858359174e-07 1.23285989366528e-06 +TR1678|c0_g1_i1 wt_37 wt_ph8 -3.62458577193226 9.02581543875671 1.43837087677047e-05 3.90414952266271e-05 +TR127|c1_g1_i1 wt_37 wt_ph8 2.90111481011278 9.73961125813442 2.21824302925283e-05 5.61954900744051e-05 +TR1894|c2_g1_i1 wt_37 wt_ph8 2.85359093751189 9.70265145133598 3.82707393478771e-05 9.08930059512081e-05 +TR5055|c0_g2_i1 wt_37 wt_ph8 1.8545312748531 10.5508309427169 0.000561739096452478 0.0012556520979526 +TR2090|c0_g1_i1 wt_37 wt_ph8 -5.85461418677349 8.72713197001274 0.000625444406369261 0.00132038263566844 +TR4859|c0_g1_i1 wt_37 wt_ph8 2.31469487039419 9.12085022188999 0.00236706272759891 0.00473412545519782 +TR1492|c0_g1_i2 wt_37 wt_ph8 0.847097868783511 16.8160271449712 0.00265383515294934 0.00504228679060374 +TR3638|c0_g1_i1 wt_37 wt_ph8 0.812580107843708 15.3469752226999 0.00403607816905259 0.00730337954399992 +TR3807|c0_g1_i1 wt_37 wt_ph8 2.92018331334326 8.37863764275674 0.0119536481076316 0.0206472103677272 +TR1449|c0_g1_i1 wt_37 wt_ph8 0.576747771663695 13.7363876885022 0.0130185393324759 0.0215088910710471 +TR1982|c2_g1_i1 wt_37 wt_ph8 -1.11743546508384 9.86122459596308 0.024471659211255 0.0382656346855499 +TR2672|c0_g1_i1 wt_37 wt_ph8 1.09825528852042 10.4080374441724 0.025174759661546 0.0382656346855499 +TR3249|c0_g1_i1 wt_37 wt_ph8 -2.00776956676821 8.66772655901099 0.0275363688345113 0.0402454621427472 +TR5212|c0_g1_i1 wt_37 wt_ph8 -0.582012857882519 12.8600915149255 0.0318599127004672 0.0448398771339909 +TR4163|c0_g1_i1 wt_37 wt_ph8 0.585935901552979 14.6858409740027 0.0333717283041774 0.0452902026985264 +TR2844|c0_g1_i1 wt_37 wt_ph8 -0.484938504762758 14.0537413817093 0.0410237194953782 0.0537552186491163 +TR1859|c3_g1_i1 wt_37 wt_ph8 -2.64648031785777 8.0811923384908 0.0677782555815868 0.0858524570700099 +TR2278|c0_g1_i1 wt_37 wt_ph8 0.462893051132405 15.2205527935145 0.0990317248813937 0.121393727273966 +TR3854|c0_g1_i1 wt_37 wt_ph8 -0.45233145936844 17.3656486469949 0.115995274036176 0.13774438791796 +TR3788|c0_g1_i1 wt_37 wt_ph8 -0.512277745155381 11.1125640718165 0.129462204245195 0.149077689736891 +TR939|c0_g1_i1 wt_37 wt_ph8 -0.343195417039388 13.0829763503018 0.196684960972624 0.219824368145874 +TR1837|c2_g1_i1 wt_37 wt_ph8 -2.21076601464763 7.9226544260522 0.248563909756302 0.269869387735413 +TR1122|c0_g1_i1 wt_37 wt_ph8 0.860567840252952 7.98418712954456 0.72405804618472 0.764283493194982 +TR2011|c5_g1_i1 wt_37 wt_ph8 0.075980865610854 9.27931055760989 0.901508002533997 0.925873083683564 +TR2182|c3_g2_i6 wt_37 wt_ph8 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
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results Mon Jan 22 11:27:24 2018 -0500 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results Thu Jun 14 03:11:51 2018 -0400 @@ -1,39 +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 +sampleA sampleB logFC logCPM PValue FDR +TR131|c0_g1_i1 wt_37 wt_ph8 -5.89108692370307 16.0946870940125 5.83734002581789e-38 2.2181892098108e-36 +TR4277|c0_g1_i1 wt_37 wt_ph8 4.47812345668175 17.3786096664403 2.84916418820701e-34 5.41341195759331e-33 +TR3091|c0_g1_i1 wt_37 wt_ph8 -4.37454375877296 13.9751350003907 3.03684158911717e-24 3.84666601288175e-23 +TR2779|c0_g1_i1 wt_37 wt_ph8 -2.89398117484377 15.8061264352363 2.71183962208552e-19 2.57624764098124e-18 +TR5075|c0_g1_i1 wt_37 wt_ph8 -3.21512246000432 12.8334153580766 2.25968184332879e-15 1.71735820092988e-14 +TR2107|c1_g1_i1 wt_37 wt_ph8 4.32040270723487 11.0762608486921 1.80270537224079e-11 1.14171340241917e-10 +TR4761|c0_g1_i1 wt_37 wt_ph8 2.00464775189483 16.4172477083723 4.47039820077749e-11 2.42678759470778e-10 +TR1891|c0_g1_i1 wt_37 wt_ph8 -1.89490003648365 14.4620196202787 2.60196088184267e-10 1.23593141887527e-09 +TR2122|c0_g2_i2 wt_37 wt_ph8 -1.68823123696301 14.4430864744705 9.44150971333403e-09 3.98641521229659e-08 +TR24|c0_g1_i1 wt_37 wt_ph8 -1.665273448047 13.6146325155501 3.81691570216026e-08 1.4504279668209e-07 +TR2487|c0_g1_i1 wt_37 wt_ph8 -1.57111929409713 15.8914511338271 9.80135417366341e-08 3.3859223509019e-07 +TR1479|c0_g1_i1 wt_37 wt_ph8 -1.45195340320994 14.3929474544484 4.87972014978913e-07 1.54524471409989e-06 +TR1678|c0_g1_i1 wt_37 wt_ph8 -3.32711159096413 8.62991286220581 2.09660385386406e-05 6.12853434206418e-05 +TR127|c1_g1_i1 wt_37 wt_ph8 2.68488776770857 9.36026180000128 7.01712501052362e-05 0.000190464821714212 +TR1894|c2_g1_i1 wt_37 wt_ph8 2.65840371977461 9.30640094015976 8.26981533784737e-05 0.0002095019885588 +TR2090|c0_g1_i1 wt_37 wt_ph8 -3.12073361486577 8.21515298661506 0.000232532921389064 0.000552265688299028 +TR5055|c0_g2_i1 wt_37 wt_ph8 1.75449782198233 10.3047459168783 0.000592147419555538 0.00125008899683947 +TR4084|c0_g1_i1 wt_37 wt_ph8 -0.990738086664283 13.5812840323914 0.000555059638311732 0.00124072154446152 +TR4859|c0_g1_i1 wt_37 wt_ph8 2.03844841522755 8.5557148387818 0.00395651243262557 0.00791302486525114 +TR3807|c0_g1_i1 wt_37 wt_ph8 2.27805436961797 7.32408068149202 0.00589866928719914 0.0106737825196937 +TR1492|c0_g1_i2 wt_37 wt_ph8 0.80292474159496 16.7717103141256 0.00563666782754467 0.0106737825196937 +TR1859|c3_g1_i1 wt_37 wt_ph8 -2.08358066039446 6.92308482511994 0.0165122223690091 0.0272810630444498 +TR3638|c0_g1_i1 wt_37 wt_ph8 0.765536214533451 15.2959378061905 0.00664915219564581 0.0114848992470246 +TR2672|c0_g1_i1 wt_37 wt_ph8 1.15555384827173 10.1973122527932 0.0181178874953213 0.0286866552009254 +TR3249|c0_g1_i1 wt_37 wt_ph8 -1.48866796495104 8.06119288435276 0.0485882100928285 0.065758173656721 +TR1982|c2_g1_i1 wt_37 wt_ph8 -1.06368641289493 9.64628067316551 0.0416733207176468 0.0609071610488684 +TR1837|c2_g1_i1 wt_37 wt_ph8 -1.43890969571076 6.48444225997254 0.11393330230991 0.135295796493019 +TR5212|c0_g1_i1 wt_37 wt_ph8 -0.63168831011067 12.8380836623566 0.0369371606978983 0.0561444842608054 +TR4163|c0_g1_i1 wt_37 wt_ph8 0.545743678134199 14.6411189904126 0.0480591953597162 0.065758173656721 +TR1449|c0_g1_i1 wt_37 wt_ph8 0.549932747054717 13.6939664483469 0.0501838693696029 0.065758173656721 +TR2844|c0_g1_i1 wt_37 wt_ph8 -0.508967050135572 14.0451022220879 0.0631262591502691 0.0799599282570075 +TR3854|c0_g1_i1 wt_37 wt_ph8 -0.504473372285636 17.3527799714624 0.0818779321593283 0.100366497485628 +TR1122|c0_g1_i1 wt_37 wt_ph8 0.501746583160273 6.50836597017328 0.579206371120405 0.611384502849316 +TR3788|c0_g1_i1 wt_37 wt_ph8 -0.524753873079964 11.0311382344715 0.196342217213272 0.213171550117267 +TR2278|c0_g1_i1 wt_37 wt_ph8 0.424377145183038 15.1829447141358 0.128541258915261 0.148017207235755 +TR2182|c3_g2_i6 wt_37 wt_ph8 -0.0429471548350905 7.57134083040984 0.954463369529891 0.954463369529891 +TR939|c0_g1_i1 wt_37 wt_ph8 -0.398499350568058 13.0523653134109 0.173205070507278 0.193582137625782 +TR2011|c5_g1_i1 wt_37 wt_ph8 -0.0410416962762211 8.85697121679121 0.94542366790428 0.954463369529891
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed
--- a/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results Mon Jan 22 11:27:24 2018 -0500 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results Thu Jun 14 03:11:51 2018 -0400 @@ -1,40 +1,40 @@ sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj -TR2779|c0_g1_i1 wt_GSNO wt_ph8 195.849684476753 966.924129135581 581.386906806167 -2.26327524632747 0.139880929176731 -16.1800129556472 6.97797522934818e-59 2.3027318256849e-57 -TR1891|c0_g1_i1 wt_GSNO wt_ph8 128.246229498835 343.028289972482 235.637259735659 -1.40437008666625 0.103208263182426 -13.6071477550587 3.63141533276091e-42 5.99183529905551e-41 -TR4761|c0_g1_i1 wt_GSNO wt_ph8 184.029205648389 351.782300021135 267.905752834762 -0.934295661860181 0.0925945355062913 -10.0901814210915 6.10565695161207e-24 6.71622264677328e-23 -TR24|c0_g1_i1 wt_GSNO wt_ph8 39.3724575919554 183.288101009647 111.330279300801 -2.12198385961523 0.229366226812664 -9.25150964508988 2.21344016014191e-20 1.82608813211707e-19 -TR3638|c0_g1_i1 wt_GSNO wt_ph8 174.266398355818 297.555274221606 235.910836288712 -0.755625651268871 0.0961172743232099 -7.86149687024996 3.79569918101421e-15 2.50516145946938e-14 -TR2122|c0_g2_i2 wt_GSNO wt_ph8 190.673533226329 328.707071692642 259.690302459485 -0.781951344246178 0.102125767694546 -7.65674875105918 1.90699193392882e-14 1.04884556366085e-13 -TR2278|c0_g1_i1 wt_GSNO wt_ph8 426.804298570637 315.99710709695 371.400702833793 0.428907012124225 0.105320470989525 4.07239929801383 4.65313200258197e-05 0.000219361937264579 -TR4084|c0_g1_i1 wt_GSNO wt_ph8 115.544575735664 157.970364768418 136.757470252041 -0.434913653199297 0.157209464946713 -2.76645972522529 0.00566685842046991 0.0233757909844384 -TR3788|c0_g1_i1 wt_GSNO wt_ph8 128.115824993653 24.010679388938 76.0632521912957 1.36551096405932 0.534260069919225 2.55589186043003 0.0105916029199559 0.0388358773731717 -TR1492|c0_g1_i2 wt_GSNO wt_ph8 1368.89238848897 813.514514376559 1091.20345143276 0.692062260203308 0.290167592747528 2.38504325603812 0.0170771132686324 0.0563544737864868 -TR1678|c0_g1_i1 wt_GSNO wt_ph8 0.695005959508731 7.10082184137838 3.89791390044355 -1.19229893380239 0.533516728634619 -2.23479203145837 0.0254310052417055 0.0762930157251164 -TR5075|c0_g1_i1 wt_GSNO wt_ph8 8.81552188359314 126.23137395943 67.5234479215117 -1.10768013972448 0.513345367512952 -2.15776786900981 0.0309458842036983 0.0851011815601704 -TR1479|c0_g1_i1 wt_GSNO wt_ph8 353.92669362375 305.546165789569 329.736429706659 0.210154850632672 0.101920088147959 2.06195711219939 0.0392118193266939 0.0995376952139152 -TR1859|c3_g1_i1 wt_GSNO wt_ph8 0 2.05957798928713 1.02978899464357 -1.01742987508067 0.500302018271162 -2.03363136250477 0.0419887772494581 1 -TR2844|c0_g1_i1 wt_GSNO wt_ph8 220.566338218013 194.214843050373 207.390590634193 0.185176880395552 0.100284765132021 1.84651058564851 0.0648181037840442 0.152785530348104 -TR2107|c1_g1_i1 wt_GSNO wt_ph8 7.08292121571621 1.78415791317121 4.43353956444371 0.951944042839851 0.540599552522162 1.76090423752399 0.0782546125949942 0.170760316089935 -TR4669|c0_g2_i1 wt_GSNO wt_ph8 165.630009730314 0 82.8150048651569 0.762969565911357 0.439826422982926 1.73470607049221 0.0827928805284532 0.170760316089935 -TR2672|c0_g1_i1 wt_GSNO wt_ph8 2.07518941673641 7.44710458698621 4.76114700186131 -0.686459125319668 0.52860452101472 -1.29862514986048 0.194072602638997 0.376729169828641 -TR4859|c0_g1_i1 wt_GSNO wt_ph8 3.10763825129944 1.1806627783491 2.14415051482427 0.593225714064679 0.537217960853533 1.10425517628294 0.269482460872864 0.494051178266917 -TR3091|c0_g1_i1 wt_GSNO wt_ph8 312.47018793986 293.531643106953 303.000915523406 0.0878939148373507 0.0878811164283744 1.00014563320878 0.317240035048796 0.536180698490786 -TR4163|c0_g1_i1 wt_GSNO wt_ph8 221.469120691076 207.118822998308 214.293971844692 0.0959413488001967 0.0974696330347526 0.984320406397642 0.324957999085325 0.536180698490786 -TR1894|c2_g1_i1 wt_GSNO wt_ph8 2.85762748931802 1.47338219762144 2.16550484346973 0.431530486406946 0.537372709941065 0.803037590900872 0.421953007665329 0.663069012045517 -TR3249|c0_g1_i1 wt_GSNO wt_ph8 2.06512931203634 4.15451161800812 3.10982046502223 -0.38612563978518 0.523142120053183 -0.738089373774619 0.460460140618999 0.675718500003336 -TR5212|c0_g1_i1 wt_GSNO wt_ph8 102.736339436612 86.4452993262187 94.5908193814151 0.226915890105892 0.314756340859895 0.720925556212693 0.470955318184143 0.675718500003336 -TR1122|c0_g1_i1 wt_GSNO wt_ph8 1.29006258579706 0.5946183773076 0.942340481552333 0.279366026492593 0.486443515520964 0.57430311552905 0.565762701275693 1 -TR2011|c5_g1_i1 wt_GSNO wt_ph8 7.597917075274 4.42090354598533 6.00941031062966 0.293830308686626 0.525066976727929 0.559605386950241 0.575748629670957 0.791654365797565 -TR1837|c2_g1_i1 wt_GSNO wt_ph8 2.16507864525674 1.46465683073113 1.81486773799393 0.232644077202222 0.530765383353658 0.438318105322267 0.661155703054792 1 -TR1982|c2_g1_i1 wt_GSNO wt_ph8 5.5352448786851 10.687042573374 8.11114372602957 -0.163617497783336 0.41190705551325 -0.397219459082736 0.691205633846634 0.874699343226649 -TR1449|c0_g1_i1 wt_GSNO wt_ph8 98.9943307118646 106.843279101242 102.918804906553 -0.100378154615576 0.259464578599584 -0.38686650469729 0.69885503944156 0.874699343226649 -TR2182|c3_g2_i6 wt_GSNO wt_ph8 1.29006258579706 1.76655578876639 1.52830918728173 -0.199699696686908 0.518464312092113 -0.385175395932417 0.700107470922461 1 -TR4277|c0_g1_i1 wt_GSNO wt_ph8 153.969096204861 149.159426886469 151.564261545665 0.0459499001744168 0.126145529370448 0.364261027748966 0.715663099003622 0.874699343226649 -TR3854|c0_g1_i1 wt_GSNO wt_ph8 2260.55060252051 1927.46472630351 2094.00766441201 0.149461409336011 0.515737174792397 0.289801504799756 0.771968096584582 0.909819542403257 -TR127|c1_g1_i1 wt_GSNO wt_ph8 1.20754470361908 1.49113571265046 1.34934020813477 -0.140499936513031 0.525109891787989 -0.267562921038549 0.789035775295455 1 -TR2090|c0_g1_i1 wt_GSNO wt_ph8 9.46045896251181 5.6546754787973 7.55756722065455 0.0558182109444541 0.287850208274631 0.193914089133468 0.846243151562143 0.956832805790417 -TR3807|c0_g1_i1 wt_GSNO wt_ph8 0.347502979754365 0.292870809896544 0.320186894825454 0.0816135421729034 0.465942705668376 0.175157892118586 0.860955569985101 1 -TR131|c0_g1_i1 wt_GSNO wt_ph8 1275.67603302799 1312.2934796972 1293.9847563626 -0.035805337908038 0.355352253126282 -0.100760126305753 0.919740880292126 0.956832805790417 -TR5055|c0_g2_i1 wt_GSNO wt_ph8 5.17791343714095 5.60171771495863 5.38981557604979 -0.0489219520111245 0.535247232645477 -0.091400663146498 0.927174234841818 0.956832805790417 -TR939|c0_g1_i1 wt_GSNO wt_ph8 92.2508462008296 94.0990807885678 93.1749634946987 -0.0260132924520656 0.31360944301959 -0.0829480522065804 0.933892845523313 0.956832805790417 -TR2487|c0_g1_i1 wt_GSNO wt_ph8 875.181494043204 882.631049341941 878.906271692572 -0.0117684251443531 0.217416529127567 -0.0541284749212796 0.956832805790417 0.956832805790417 +TR2779|c0_g1_i1 wt_GSNO wt_ph8 195.849684476753 966.924129135581 581.386906806167 -2.30255444666643 0.142496869452374 -16.1586318037394 9.87286349195067e-59 3.65295949202175e-57 +TR1891|c0_g1_i1 wt_GSNO wt_ph8 128.246229498835 343.028289972482 235.637259735659 -1.41742353970608 0.104322254921725 -13.5869718380762 4.7847024102546e-42 8.85169945897101e-41 +TR4761|c0_g1_i1 wt_GSNO wt_ph8 184.029205648389 351.782300021135 267.905752834762 -0.941259207260894 0.0933372308442124 -10.0844989587481 6.46943903995441e-24 7.97897481594377e-23 +TR24|c0_g1_i1 wt_GSNO wt_ph8 39.3724575919554 183.288101009647 111.330279300801 -2.22846767043702 0.242443002218043 -9.19171784728532 3.8661704482204e-20 3.57620766460387e-19 +TR3638|c0_g1_i1 wt_GSNO wt_ph8 174.266398355818 297.555274221606 235.910836288712 -0.761689698593786 0.0969314803260852 -7.85802193499368 3.90246977317854e-15 2.88782763215212e-14 +TR2122|c0_g2_i2 wt_GSNO wt_ph8 190.673533226329 328.707071692642 259.690302459485 -0.789061688115738 0.103094089827306 -7.65380139091878 1.95123561208803e-14 1.20326196078762e-13 +TR4669|c0_g2_i1 wt_GSNO wt_ph8 165.630009730314 0 82.8150048651569 9.98638581786287 2.4059110197361 4.15077105343582 3.31357095211564e-05 0.000175145893183255 +TR2278|c0_g1_i1 wt_GSNO wt_ph8 426.804298570637 315.99710709695 371.400702833793 0.433055347501052 0.106340324733669 4.07235306630524 4.65405596936774e-05 0.000215250088583258 +TR4084|c0_g1_i1 wt_GSNO wt_ph8 115.544575735664 157.970364768418 136.757470252041 -0.444508945050626 0.160721197310781 -2.76571449496544 0.00567982380522758 0.0233503867548245 +TR3788|c0_g1_i1 wt_GSNO wt_ph8 128.115824993653 24.010679388938 76.0632521912957 2.41599826196159 0.930388620648254 2.59676248004649 0.00941069736444863 0.0348195802484599 +TR5075|c0_g1_i1 wt_GSNO wt_ph8 8.81552188359314 126.23137395943 67.5234479215117 -3.83892667969009 1.51640337447055 -2.53159993199728 0.011354345783228 0.0381918903617669 +TR1492|c0_g1_i2 wt_GSNO wt_ph8 1368.89238848897 813.514514376559 1091.20345143276 0.750717599362045 0.314762309207928 2.38503015577424 0.0170777214032423 0.0526563076599971 +TR1678|c0_g1_i1 wt_GSNO wt_ph8 0.695005959508731 7.10082184137838 3.89791390044355 -3.29023865439926 1.5074251817588 -2.18268786684349 0.0290588040465388 0.0827058269016874 +TR1479|c0_g1_i1 wt_GSNO wt_ph8 353.92669362375 305.546165789569 329.736429706659 0.212056310257658 0.102841330599285 2.0619755600394 0.0392100628615421 0.0987833713777749 +TR1859|c3_g1_i1 wt_GSNO wt_ph8 0 2.05957798928713 1.02978899464357 -3.32897459707672 1.62131131542189 -2.05326057087961 0.0400473127207196 0.0987833713777749 +TR2844|c0_g1_i1 wt_GSNO wt_ph8 220.566338218013 194.214843050373 207.390590634193 0.186796872895526 0.101161116569868 1.84652838194517 0.0648155222548659 0.149885895214377 +TR2107|c1_g1_i1 wt_GSNO wt_ph8 7.08292121571621 1.78415791317121 4.43353956444371 1.99039306371489 1.13345482120555 1.75604093473959 0.0790814192380851 0.172118383047597 +TR2672|c0_g1_i1 wt_GSNO wt_ph8 2.07518941673641 7.44710458698621 4.76114700186131 -1.80710364026684 1.37881760417113 -1.31061834052603 0.189986739707575 0.390528298287793 +TR4859|c0_g1_i1 wt_GSNO wt_ph8 3.10763825129944 1.1806627783491 2.14415051482427 1.36600125700608 1.2414304168313 1.10034460126467 0.271182006077654 0.528091274993326 +TR3091|c0_g1_i1 wt_GSNO wt_ph8 312.47018793986 293.531643106953 303.000915523406 0.0884824617062972 0.0884687505769758 1.00015498273946 0.317235511103454 0.572534846407878 +TR4163|c0_g1_i1 wt_GSNO wt_ph8 221.469120691076 207.118822998308 214.293971844692 0.0967338751775769 0.0982736079923787 0.984332183927538 0.32495221012339 0.572534846407878 +TR1894|c2_g1_i1 wt_GSNO wt_ph8 2.85762748931802 1.47338219762144 2.16550484346973 0.974874448083219 1.21963227734233 0.799318340612911 0.424105846774723 0.713268924121126 +TR3249|c0_g1_i1 wt_GSNO wt_ph8 2.06512931203634 4.15451161800812 3.10982046502223 -1.06280923847799 1.42172379433194 -0.747549729923031 0.454731796166148 0.726065302514322 +TR5212|c0_g1_i1 wt_GSNO wt_ph8 102.736339436612 86.4452993262187 94.5908193814151 0.250307109752951 0.347207101059694 0.720915871216346 0.470961277306587 0.726065302514322 +TR1122|c0_g1_i1 wt_GSNO wt_ph8 1.29006258579706 0.5946183773076 0.942340481552333 1.01745920560278 1.75106315862361 0.581052259932493 0.56120523253296 1 +TR2011|c5_g1_i1 wt_GSNO wt_ph8 7.597917075274 4.42090354598533 6.00941031062966 0.776221433822186 1.38068634268934 0.562199689981896 0.573979972628347 0.849490359489954 +TR1837|c2_g1_i1 wt_GSNO wt_ph8 2.16507864525674 1.46465683073113 1.81486773799393 0.574055870722254 1.31330872914193 0.437106567545105 0.662034064585522 0.882648546299865 +TR1982|c2_g1_i1 wt_GSNO wt_ph8 5.5352448786851 10.687042573374 8.11114372602957 -0.948745824078601 2.34310116245329 -0.404910312572778 0.685543437736556 0.882648546299865 +TR2182|c3_g2_i6 wt_GSNO wt_ph8 1.29006258579706 1.76655578876639 1.52830918728173 -0.570835750385155 1.46441538912588 -0.389804528567464 0.69668109483689 0.882648546299865 +TR1449|c0_g1_i1 wt_GSNO wt_ph8 98.9943307118646 106.843279101242 102.918804906553 -0.106933839690288 0.276431863357554 -0.386836156988073 0.69887750768045 0.882648546299865 +TR4277|c0_g1_i1 wt_GSNO wt_ph8 153.969096204861 149.159426886469 151.564261545665 0.0465928591854992 0.127909639606222 0.364263861026723 0.715660983486377 0.882648546299865 +TR3854|c0_g1_i1 wt_GSNO wt_ph8 2260.55060252051 1927.46472630351 2094.00766441201 0.229965172704227 0.793466242289153 0.289823511635197 0.771951259799022 0.910963182508483 +TR127|c1_g1_i1 wt_GSNO wt_ph8 1.20754470361908 1.49113571265046 1.34934020813477 -0.373671738849606 1.38864714646401 -0.269090488394483 0.787860049737066 0.910963182508483 +TR2090|c0_g1_i1 wt_GSNO wt_ph8 9.46045896251181 5.6546754787973 7.55756722065455 0.740040477295998 3.75055668025179 0.197314836272869 0.843581169905129 0.945833432923932 +TR3807|c0_g1_i1 wt_GSNO wt_ph8 0.347502979754365 0.292870809896544 0.320186894825454 0.331202385322154 1.89086385045429 0.175159298350635 0.86095446505486 1 +TR131|c0_g1_i1 wt_GSNO wt_ph8 1275.67603302799 1312.2934796972 1293.9847563626 -0.0408368749216097 0.405274721880973 -0.100763439506112 0.919738250126613 0.956831887096638 +TR5055|c0_g2_i1 wt_GSNO wt_ph8 5.17791343714095 5.60171771495863 5.38981557604979 -0.113901914254779 1.2463123048955 -0.0913911495596841 0.927181793948424 0.956831887096638 +TR939|c0_g1_i1 wt_GSNO wt_ph8 92.2508462008296 94.0990807885678 93.1749634946987 -0.0286723936076206 0.345661698999542 -0.0829492931690373 0.933891858779013 0.956831887096638 +TR2487|c0_g1_i1 wt_GSNO wt_ph8 875.181494043204 882.631049341941 878.906271692572 -0.0122873741271452 0.226999049805604 -0.0541296280212089 0.956831887096638 0.956831887096638
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.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset Thu Jun 14 03:11:51 2018 -0400 @@ -0,0 +1,1 @@ +sampleA sampleB 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/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset Thu Jun 14 03:11:51 2018 -0400 @@ -0,0 +1,3 @@ +sampleA sampleB 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 wt_GSNO wt_ph8 195.849684476753 966.924129135581 581.386906806167 -2.26327524632747 0.139880929176731 -16.1800129556472 6.97797522934818e-59 2.3027318256849e-57 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00 +TR24|c0_g1_i1 wt_GSNO wt_ph8 39.3724575919554 183.288101009647 111.330279300801 -2.12198385961523 0.229366226812664 -9.25150964508988 2.21344016014191e-20 1.82608813211707e-19 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00
--- a/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results Mon Jan 22 11:27:24 2018 -0500 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results Thu Jun 14 03:11:51 2018 -0400 @@ -1,40 +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 +sampleA sampleB logFC logCPM PValue FDR +TR2779|c0_g1_i1 wt_GSNO wt_ph8 -2.23948335958727 15.9163308249372 1.20766376889896e-237 4.70988869870595e-236 +TR1492|c0_g1_i2 wt_GSNO wt_ph8 0.807859120941235 16.8439348559211 2.37986391219743e-61 4.64073462878498e-60 +TR1891|c0_g1_i1 wt_GSNO wt_ph8 -1.35697452203657 14.6311197032228 1.60645028176433e-35 2.08838536629363e-34 +TR4761|c0_g1_i1 wt_GSNO wt_ph8 -0.880921757190946 14.8138260614735 1.59143301924913e-24 1.5516471937679e-23 +TR2122|c0_g2_i2 wt_GSNO wt_ph8 -0.729785350305026 14.7699678361852 6.52776857951534e-13 5.09165949202196e-12 +TR3854|c0_g1_i1 wt_GSNO wt_ph8 0.289859344737128 17.7786469452325 6.1302236270955e-12 3.98464535761207e-11 +TR3638|c0_g1_i1 wt_GSNO wt_ph8 -0.702510801497461 14.6355179638282 5.62335492840333e-11 3.133012031539e-10 +TR2278|c0_g1_i1 wt_GSNO wt_ph8 0.490901034745758 15.2921454021456 1.53296499052609e-09 7.47320432881468e-09 +TR24|c0_g1_i1 wt_GSNO wt_ph8 -2.16007337608378 13.5636496776551 8.67157466173412e-09 3.75768235341812e-08 +TR5075|c0_g1_i1 wt_GSNO wt_ph8 -3.7524485458028 12.8683202800317 5.50095216588421e-08 2.14537134469484e-07 +TR4669|c0_g2_i1 wt_GSNO wt_ph8 10.4044948993067 13.1110475123695 1.35189372056785e-06 4.79307773655872e-06 +TR3788|c0_g1_i1 wt_GSNO wt_ph8 2.47698512550917 13.0240883091698 1.80487840553907e-05 5.86585481800198e-05 +TR1479|c0_g1_i1 wt_GSNO wt_ph8 0.272661827455658 15.1172528121102 0.000483095512098729 0.00144928653629619 +TR1678|c0_g1_i1 wt_GSNO wt_ph8 -3.02812287247775 9.36059212330112 0.0074853976481696 0.0208521791627582 +TR2107|c1_g1_i1 wt_GSNO wt_ph8 1.98032359155541 9.36544178725855 0.0305238827180189 0.0756824353198294 +TR2844|c0_g1_i1 wt_GSNO wt_ph8 0.244755727600329 14.4560017424587 0.0310492042337762 0.0756824353198294 +TR1859|c3_g1_i1 wt_GSNO wt_ph8 -4.12978123132011 8.37588761488442 0.0428877609330621 0.0983895691993777 +TR3091|c0_g1_i1 wt_GSNO wt_ph8 0.148576217250104 14.9963238698071 0.0547318692708507 0.11858571675351 +TR2672|c0_g1_i1 wt_GSNO wt_ph8 -1.64029381826409 9.53984158811941 0.100507062957769 0.206303971334369 +TR4163|c0_g1_i1 wt_GSNO wt_ph8 0.156926020788278 14.5006265631178 0.113620071038851 0.22155913852576 +TR4859|c0_g1_i1 wt_GSNO wt_ph8 1.3062724221166 8.73091245897321 0.181160758857669 0.3364414093071 +TR4084|c0_g1_i1 wt_GSNO wt_ph8 -0.390578563212142 13.8603174460746 0.270419882900116 0.479380701504752 +TR1982|c2_g1_i1 wt_GSNO wt_ph8 -0.866592651710305 10.0958159836705 0.312186869456376 0.515984430920105 +TR1894|c2_g1_i1 wt_GSNO wt_ph8 0.989932992780787 8.78384403630691 0.317528880566218 0.515984430920105 +TR4277|c0_g1_i1 wt_GSNO wt_ph8 0.107189584823599 14.0046148411409 0.347278576725125 0.541754579691195 +TR2487|c0_g1_i1 wt_GSNO wt_ph8 0.0467513454249246 16.526653433485 0.376403968202147 0.560230359736405 +TR3249|c0_g1_i1 wt_GSNO wt_ph8 -1.00369455926223 9.08504250192555 0.387851787509819 0.560230359736405 +TR5212|c0_g1_i1 wt_GSNO wt_ph8 0.310409394484433 13.3365591825697 0.416163942507532 0.572783249883747 +TR2011|c5_g1_i1 wt_GSNO wt_ph8 0.799376994792807 9.70509536731836 0.425915749913555 0.572783249883747 +TR1837|c2_g1_i1 wt_GSNO wt_ph8 0.59484087321072 8.66193471010726 0.588495494688377 0.76504414309489 +TR2090|c0_g1_i1 wt_GSNO wt_ph8 0.766971023107968 9.89421471118339 0.638322407555079 0.8030507707951 +TR131|c0_g1_i1 wt_GSNO wt_ph8 0.0187996511046741 17.0827735361623 0.697507705031756 0.850087515507453 +TR1122|c0_g1_i1 wt_GSNO wt_ph8 0.908051089281089 8.22928258978683 0.753364106379395 0.890339398448377 +TR1449|c0_g1_i1 wt_GSNO wt_ph8 -0.0452741219590205 13.4583026590017 0.919111339143084 1 +TR939|c0_g1_i1 wt_GSNO wt_ph8 0.0309689709592036 13.3146949564453 0.956245904999637 1 +TR5055|c0_g2_i1 wt_GSNO wt_ph8 -0.0548476287872344 9.62768102188797 0.999999999999985 1 +TR2182|c3_g2_i6 wt_GSNO wt_ph8 -0.517423422896207 8.5297276065799 1 1 +TR127|c1_g1_i1 wt_GSNO wt_ph8 -0.299043611515333 8.4576897025083 1 1 +TR3807|c0_g1_i1 wt_GSNO wt_ph8 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
--- a/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results Mon Jan 22 11:27:24 2018 -0500 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results Thu Jun 14 03:11:51 2018 -0400 @@ -1,40 +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 +sampleA sampleB logFC logCPM PValue FDR +TR2779|c0_g1_i1 wt_GSNO wt_ph8 -2.23795519272237 15.9076254017254 2.92187316761645e-09 1.13953053537042e-07 +TR1492|c0_g1_i2 wt_GSNO wt_ph8 0.807554446371668 16.8426446227048 5.58321346448906e-08 1.08872662557537e-06 +TR24|c0_g1_i1 wt_GSNO wt_ph8 -2.16839334936064 13.5222768601527 3.73856822091501e-07 4.86013868718952e-06 +TR3788|c0_g1_i1 wt_GSNO wt_ph8 2.47096654484901 13.0144557887788 1.245732049043e-06 9.71670998253539e-06 +TR5075|c0_g1_i1 wt_GSNO wt_ph8 -3.68481140303272 12.7944067233298 3.44359702134355e-06 2.23833806387331e-05 +TR3854|c0_g1_i1 wt_GSNO wt_ph8 0.290746293924475 17.7782076349597 5.25322144866517e-07 5.12189091244854e-06 +TR1891|c0_g1_i1 wt_GSNO wt_ph8 -1.35768165107067 14.6117632515968 5.28666359293828e-06 2.79053243123467e-05 +TR4761|c0_g1_i1 wt_GSNO wt_ph8 -0.878920056028248 14.8002262876656 5.72416908971214e-06 2.79053243123467e-05 +TR2122|c0_g2_i2 wt_GSNO wt_ph8 -0.730166040402744 14.7551588447381 0.000213340170514583 0.000924474072229861 +TR3638|c0_g1_i1 wt_GSNO wt_ph8 -0.708321413581678 14.6195575978943 0.000258928735946659 0.00100982207019197 +TR2107|c1_g1_i1 wt_GSNO wt_ph8 1.90861736829884 8.90712643491077 0.00457979737107378 0.0148843414559898 +TR1678|c0_g1_i1 wt_GSNO wt_ph8 -2.86408187112217 8.67828416118206 0.00614682516189 0.01844047548567 +TR2278|c0_g1_i1 wt_GSNO wt_ph8 0.503051556783977 15.2850549214884 0.00155857674629228 0.00552586300958173 +TR1859|c3_g1_i1 wt_GSNO wt_ph8 -1.96144637998691 6.77065030795652 0.0428269385052548 0.0982500353944082 +TR2672|c0_g1_i1 wt_GSNO wt_ph8 -1.69730734417424 8.97832173338033 0.0866262290356731 0.160877282494822 +TR1479|c0_g1_i1 wt_GSNO wt_ph8 0.277933522953326 15.1098597149167 0.0157877120065803 0.0439800548754737 +TR1982|c2_g1_i1 wt_GSNO wt_ph8 -0.859948395691952 9.74982883974683 0.0845253825418736 0.160877282494822 +TR4859|c0_g1_i1 wt_GSNO wt_ph8 1.04376243585308 7.84838377560073 0.178339170085147 0.289801151388364 +TR2011|c5_g1_i1 wt_GSNO wt_ph8 0.835627288758852 9.33803398810951 0.117576176969539 0.20843049553691 +TR4084|c0_g1_i1 wt_GSNO wt_ph8 -0.383433512314591 13.8345091917852 0.0320674039619619 0.083375250301101 +TR1894|c2_g1_i1 wt_GSNO wt_ph8 0.899367664455804 7.86698528437277 0.236693956821629 0.369242572641742 +TR5212|c0_g1_i1 wt_GSNO wt_ph8 0.317453614519532 13.3093804544918 0.0408068910563242 0.0982500353944082 +TR2182|c3_g2_i6 wt_GSNO wt_ph8 -0.988859576038597 7.34392475064937 0.332144974966109 0.462630500845651 +TR3249|c0_g1_i1 wt_GSNO wt_ph8 -1.18548803762213 8.36747688877935 0.296376188714782 0.444564283072173 +TR1837|c2_g1_i1 wt_GSNO wt_ph8 0.83411458992077 7.6102620160458 0.393260306376011 0.528867308574635 +TR3807|c0_g1_i1 wt_GSNO wt_ph8 0.40219136988549 5.09566487188118 0.681998347783062 0.765740423023185 +TR4669|c0_g2_i1 wt_GSNO wt_ph8 6.05037553674292 13.1239272719772 0.480074268471172 0.603964402270185 +TR1122|c0_g1_i1 wt_GSNO wt_ph8 0.184244267394782 6.64199260311611 0.869699168726351 0.892585988955992 +TR127|c1_g1_i1 wt_GSNO wt_ph8 -0.354388761220407 7.15556768591471 0.687202943738756 0.765740423023185 +TR2844|c0_g1_i1 wt_GSNO wt_ph8 0.251980888130202 14.4425124782726 0.0594765231313145 0.128865800117848 +TR2090|c0_g1_i1 wt_GSNO wt_ph8 -0.862128177746631 9.64998833298881 0.646749723219784 0.764340581987017 +TR3091|c0_g1_i1 wt_GSNO wt_ph8 0.148831558112849 14.9878570236746 0.0841354210369957 0.160877282494822 +TR5055|c0_g2_i1 wt_GSNO wt_ph8 0.0583511298028353 9.18288041060754 0.918331019801174 0.918331019801174 +TR4163|c0_g1_i1 wt_GSNO wt_ph8 0.161834057105857 14.4879250602579 0.126768900432688 0.214955961603254 +TR4277|c0_g1_i1 wt_GSNO wt_ph8 0.103273026252208 13.9874746529507 0.30829078508145 0.445308911784317 +TR939|c0_g1_i1 wt_GSNO wt_ph8 0.0333503331526365 13.2856573711711 0.715260879184748 0.774865952450143 +TR1449|c0_g1_i1 wt_GSNO wt_ph8 -0.049884213852527 13.4293306544833 0.75234222467997 0.793009371959969 +TR2487|c0_g1_i1 wt_GSNO wt_ph8 0.0480185034754555 16.5239765307922 0.407818984620182 0.530164680006236 +TR131|c0_g1_i1 wt_GSNO wt_ph8 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
Binary file test-data/count/qcheck/input.matrix.CPM.log2.prcomp.principal_components.pdf has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/norm/Trinity_paired_unmerged_1.fasta Thu Jun 14 03:11:51 2018 -0400 @@ -0,0 +1,14 @@ +>TRINITY_DN2_c0_g1_i1 len=229 path=[0:0-228] +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC +>TRINITY_DN1_c0_g1_i1 len=380 path=[0:0-379] +CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATGTATATGGTACAGATGTAAAG +>TRINITY_DN3_c0_g1_i1 len=669 path=[0:0-668] +GCTGCATCAGACCAAGATGAAAGCATAGTAGAACTTGCATTTCAGACAACAGGGCACATTGTCACTCTTGTATTTGAAAAACACTTTCCGGCCACCATTGATTCTTTCCAGGATGCAGTGAAGTGTTTGTCTGAATTCACATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTG +>TRINITY_DN3_c0_g2_i1 len=279 path=[0:0-278] +TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA +>TRINITY_DN3_c0_g3_i1 len=240 path=[0:0-239] +ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGAGTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGCTACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC +>TRINITY_DN3_c0_g4_i1 len=202 path=[0:0-201] +GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACCAA +>TRINITY_DN0_c0_g1_i1 len=216 path=[0:0-215] +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/norm/Trinity_paired_unmerged_1.map Thu Jun 14 03:11:51 2018 -0400 @@ -0,0 +1,7 @@ +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 +TRINITY_DN3_c0_g2 TRINITY_DN3_c0_g2_i1 +TRINITY_DN3_c0_g3 TRINITY_DN3_c0_g3_i1 +TRINITY_DN3_c0_g4 TRINITY_DN3_c0_g4_i1 +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1
--- a/test-data/raw/Trinity.fasta Mon Jan 22 11:27:24 2018 -0500 +++ b/test-data/raw/Trinity.fasta Thu Jun 14 03:11:51 2018 -0400 @@ -43,4 +43,3 @@ CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw/Trinity_single_unmerged_1.fasta Thu Jun 14 03:11:51 2018 -0400 @@ -0,0 +1,2 @@ +>TRINITY_DN0_c0_g1_i1 len=226 path=[0:0-225] +CTTTACATCTGTACCATATACATATCCACCTGAAAACATTTTCTACATCCACTGTTATATGGAATGCTTGATAAGCTTTTCATTCTAACCATCAGAGCACAGTTCACAGTATGAATACATTTCCAGTAAATCTAACCTCCCAAAACCATGCCAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATCTACATCAAGCCCCGCCACCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw/Trinity_single_unmerged_1.map Thu Jun 14 03:11:51 2018 -0400 @@ -0,0 +1,1 @@ +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/supertranscripts/trinity_genes.fasta Thu Jun 14 03:11:51 2018 -0400 @@ -0,0 +1,14 @@ +>TRINITY_DN1_c0_g1 +CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATGTATATGGTACAGATGTAAAG +>TRINITY_DN0_c0_g1 +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC +>TRINITY_DN2_c0_g1 +TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA +>TRINITY_DN2_c1_g1 +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTG +>TRINITY_DN2_c2_g1 +ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGAGTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGCTACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC +>TRINITY_DN2_c3_g1 +GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACCAA +>TRINITY_DN3_c0_g1 +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/supertranscripts/trinity_genes.gtf Thu Jun 14 03:11:51 2018 -0400 @@ -0,0 +1,14 @@ +TRINITY_DN1_c0_g1 Trinity_gene exon 1 380 . + . gene_id "TRINITY_DN1_c0_g1"; transcript_id "TRINITY_DN1_c0_g1_i1" + +TRINITY_DN0_c0_g1 Trinity_gene exon 1 229 . + . gene_id "TRINITY_DN0_c0_g1"; transcript_id "TRINITY_DN0_c0_g1_i1" + +TRINITY_DN2_c0_g1 Trinity_gene exon 1 279 . + . gene_id "TRINITY_DN2_c0_g1"; transcript_id "TRINITY_DN2_c0_g1_i1" + +TRINITY_DN2_c1_g1 Trinity_gene exon 1 541 . + . gene_id "TRINITY_DN2_c1_g1"; transcript_id "TRINITY_DN2_c1_g1_i1" + +TRINITY_DN2_c2_g1 Trinity_gene exon 1 240 . + . gene_id "TRINITY_DN2_c2_g1"; transcript_id "TRINITY_DN2_c2_g1_i1" + +TRINITY_DN2_c3_g1 Trinity_gene exon 1 202 . + . gene_id "TRINITY_DN2_c3_g1"; transcript_id "TRINITY_DN2_c3_g1_i1" + +TRINITY_DN3_c0_g1 Trinity_gene exon 1 216 . + . gene_id "TRINITY_DN3_c0_g1"; transcript_id "TRINITY_DN3_c0_g1_i1" +