Mercurial > repos > iuc > trinity_super_transcripts
changeset 0:64094e19077d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,30 @@ +Trinity memory usage +==================== + +As described on the official Trinity website +`FAQ <http://trinityrnaseq.sourceforge.net/trinity_faq.html#ques_comp_resources_required>`_, +trinity requires a large amount of memory to perform the assembly: "roughly +~1G of RAM per 1M reads to be assembled" + +By default, this tool is configured to limit the memory consumption to 1G. +You might need to lower this limit if the machine(s) executing the jobs have less memory available. +If you have a lot of reads to assemble and a machine with enough memory, you can increase it. +In both cases, you can set the GALAXY_MEMORY_MB environmental variable in the destination section of the job_conf.xml file:: + + <?xml version="1.0"?> + <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --> + <job_conf> + <plugins> + <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> + </plugins> + <handlers> + <handler id="main"/> + </handlers> + <destinations> + <destination id="local" runner="local"> + <env id="GALAXY_MEMORY_MB">1G</env> + </destination> + </destinations> + </job_conf> + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,39 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.6.6">trinity</requirement> + <yield/> + </requirements> + </xml> + + <token name="@WRAPPER_VERSION@">2.6.6</token> + + <token name="@COMMAND_PAIRED_STRAND_JACCARD@"> + #if $pool.inputs.strand.is_strand_specific: + --SS_lib_type $pool.inputs.strand.library_type + #end if + + $pool.inputs.jaccard_clip + </token> + + <xml name="input_paired_strand_jaccard"> + <conditional name="strand"> + <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> + <when value="false" /> + <when value="true"> + <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type"> + <option value="FR">Forward-Reverse</option> + <option value="RF">Reverse-Forward</option> + </param> + </when> + </conditional> + <param name="jaccard_clip" argument="--jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="Set if you expect high gene density with UTR overlap"/> + </xml> + + <xml name="citation"> + <citations> + <citation type="doi">10.1038/nbt.1883</citation> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/super_transcripts.xml Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,35 @@ +<tool id="trinity_super_transcripts" name="Generate SuperTranscripts" version="@WRAPPER_VERSION@"> + <description>from a Trinity assembly</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ + Trinity_gene_splice_modeler.py --incl_malign --trinity_fasta '$assembly' + ]]></command> + <inputs> + <param format="fasta" name="assembly" type="data" label="Trinity assembly"/> + </inputs> + <outputs> + <data format="fasta" name="seqs" from_work_dir="trinity_genes.fasta" label="${tool.name} on ${on_string}: SuperTranscripts sequences"/> + <data format="gtf" name="annotation" from_work_dir="trinity_genes.gtf" label="${tool.name} on ${on_string}: SuperTranscripts strcture annotation"/> + <data format="clustal" name="malign" from_work_dir="trinity_genes.malign" label="${tool.name} on ${on_string}: multiple alignment of SuperTranscripts"/> + </outputs> + <tests> + <test> + <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/> + <output name="seqs" file="supertranscripts/trinity_genes.fasta" /> + <output name="annotation" file="supertranscripts/trinity_genes.gtf" /> + <output name="malign" file="supertranscripts/trinity_genes.malign" /> + </test> + </tests> + <help> + SuperTranscripts provide a gene-like view of the transcriptional complexity of a gene. SuperTranscripts were originally defined by Nadia Davidson, Anthony Hawkins, and Alicia Oshlack as described in their publication "SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes" Genome Biology, 2017. SuperTranscripts are useful in the context of genome-free de novo transcriptome assembly in that they provide a genome-like reference for studying aspects of the gene including differential transcript usage (aka. differential exon usage) and as a substrate for mapping reads and identifying allelic polymorphisms. + + A SuperTranscript is constructed by collapsing unique and common sequence regions among splicing isoforms into a single linear sequence. + + .. _Trinity: http://trinityrnaseq.github.io + </help> + + <expand macro="citation" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/Trinity.map Thu Jun 14 03:12:34 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_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,7 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR4277|c0_g1_i1 3852.97388871986 161.116814813422 2007.04535176664 -4.57259674791206 0.121601866332754 -37.6030145409076 0 0 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00 +TR4761|c0_g1_i1 1645.20640957447 193.196157329029 919.201283451752 -3.08847487551254 0.143642016580712 -21.5011940728159 1.51733402752078e-102 1.66906743027286e-101 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00 +TR2107|c1_g1_i1 48.9228907410258 7.40521775805688 28.1640542495414 -2.6949883047084 0.431525668867458 -6.24525607429428 4.23106352657394e-10 1.55138995974378e-09 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00 +TR2672|c0_g1_i1 18.3155337236093 2.26581902751323 10.2906763755613 -2.88818323474529 0.724350842979802 -3.98727117216294 6.68376171815065e-05 0.000157545811927837 14.00 29.00 22.00 0.00 4.00 2.00 14.00 4.00 7.00 +TR127|c1_g1_i1 13.461799216177 1.21881296083961 7.34030608850831 -3.33218181130749 0.914685635912973 -3.64298036448506 0.000269499403689035 0.000576210779000196 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 +TR5055|c0_g2_i1 23.3590211688541 5.52768338415684 14.4433522765055 -2.04478780320925 0.562727305023446 -3.63370994255211 0.00027937492315161 0.000576210779000196 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.depleted Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR under_represented_FDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,4 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR131|c0_g1_i1 26.1866396538608 1340.30918254958 683.247911101723 5.67372481552909 0.187406695960058 30.274931140872 2.45144211418965e-201 4.04487948841292e-200 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00 +TR3091|c0_g1_i1 16.7444693227929 328.569936894811 172.657203108802 4.29039998257063 0.240421038467916 17.8453599980735 3.14072644239509e-71 2.59109931497595e-70 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00 +TR3788|c0_g1_i1 19.5075441237117 134.95369713876 77.2306206312357 2.77038513264018 0.262760026053246 10.5434040871909 5.44900939296595e-26 2.56881871382681e-25 17.00 30.00 22.00 91.00 132.00 125.00 32.00 22.00 27.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset.GOseq.depleted Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR under_represented_FDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset.GOseq.enriched Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,7 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR4277|c0_g1_i1 4705.34614971641 162.902721493704 2434.12443560506 -4.84860951090545 0.124597307945428 -38.9142397284305 0 0 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00 +TR4761|c0_g1_i1 2012.6141923276 384.620292965437 1198.61724264652 -2.38450946693381 0.143863830576436 -16.5747669680385 1.06073316501088e-61 1.34359534234711e-60 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00 +TR2107|c1_g1_i1 59.5986596731862 1.89840873462066 30.7485342039034 -4.81058600791914 0.641850436461167 -7.49487066557473 6.63637683134955e-14 2.29256654173894e-13 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00 +TR127|c1_g1_i1 16.3791628279609 1.58772512712498 8.98344397754296 -3.19771077466237 0.834376974262452 -3.83245328346816 0.00012687169720824 0.000267840249661839 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 +TR1894|c2_g1_i1 16.2826445742552 1.67571344127509 8.97917900776516 -3.15659686337855 0.834779400611257 -3.7813545244015 0.00015597736029041 0.000307529893573321 21.00 14.00 11.00 1.00 2.00 5.00 1.00 3.00 1.00 +TR5055|c0_g2_i1 28.6665933385886 6.05959103586122 17.3630921872249 -2.17768048931004 0.577307428800381 -3.77213314894485 0.000161857838722801 0.000307529893573321 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.depleted Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR under_represented_FDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,2 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR go_term +GO:0008270 0.0469428206943769 0.996332779511344 3 6 zinc ion binding MF 0.790651800018629 MF zinc ion binding
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,5 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR131|c0_g1_i1 32.0461070493257 1436.30905989883 734.177583474076 5.48367743370229 0.196017912869615 27.9753893581648 3.23827538807456e-172 6.15272323734167e-171 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00 +TR3091|c0_g1_i1 20.4914097091341 321.651020117047 171.071214913091 3.96886910507283 0.256323110469072 15.4838519937191 4.45952081812589e-54 4.2365447772196e-53 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00 +TR2779|c0_g1_i1 191.51955185349 1058.15934185376 624.839446853626 2.46616535412611 0.177102083131526 13.9251064161374 4.4587691300744e-44 3.38866453885655e-43 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00 +TR5075|c0_g1_i1 19.3833722195684 136.98672801182 78.1850501156942 2.80049241151413 0.293976352213923 9.52625063350759 1.63066468983638e-21 8.85217974482605e-21 13.00 22.00 21.00 6.00 8.00 10.00 163.00 121.00 142.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.depleted Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR under_represented_FDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.enriched Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.DE.subset.GOseq.enriched Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,1 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,3 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR2779|c0_g1_i1 195.849684476753 966.924129135581 581.386906806167 2.25621220756415 0.156114979193812 14.4522467940961 2.42639762934434e-47 5.82335431042642e-46 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00 +TR24|c0_g1_i1 39.3724575919554 183.288101009647 111.330279300801 2.11680322693425 0.240338854880295 8.80757806717753 1.27878744153922e-18 7.67272464923531e-18 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.depleted Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR under_represented_FDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.enriched Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/results.matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,14 @@ +wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +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 +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 +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 +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 +TR1894|c2_g1_i1 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/analyze_diff_expr/results.matrix.log2.centered.dat Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,14 @@ +wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +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 +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 +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 +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 +TR1894|c2_g1_i1 2.11263053903627 1.56008951600749 1.23816142112012 -1.34680107960103 -0.761838578879876 0.238161421120124 -1.34680107960103 -0.346801079601032 -1.34680107960103
Binary file test-data/count/analyze_diff_expr/results.matrix.log2.centered.genes_vs_samples_heatmap.pdf has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/contig_exn50_statistic/ExN50.stats Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,4 @@ +Ex ExN50 num_transcripts +33 541 1 +67 541 2 +100 279 7
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/contig_exn50_statistic/Trinity.fasta Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,46 @@ +>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] +CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG +CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC +AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT +ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG +GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG +AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG +TATATGGTACAGATGTAAAG +>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT +TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT +ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA +TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC +>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] +TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA +ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC +AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG +AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA +AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA +>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT +TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA +TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT +TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT +AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT +ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA +AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC +CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG +GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT +G +>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] +ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA +GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC +TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG +TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC +>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] +GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC +AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC +CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC +ATACATGATTCTATTCAACCAA +>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG +CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT +ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA +TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/contig_exn50_statistic/matrix.TMM.EXPR.matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ + sample_A sample_B +TRINITY_DN2_c2_g1_i1 525311.050 145165.140 +TRINITY_DN2_c1_g1_i1 145165.140 525311.050 +TRINITY_DN2_c0_g1_i1 0.000 0.000 +TRINITY_DN1_c0_g1_i1 329523.810 329523.810 +TRINITY_DN3_c0_g1_i1 0.000 0.000 +TRINITY_DN2_c3_g1_i1 0.000 0.000 +TRINITY_DN0_c0_g1_i1 0.000 0.000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/define_clusters_by_cutting_tree/subcluster_1_log2_medianCentered_fpkm.matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,7 @@ +wt_37_2 wt_37_3 wt_37_1 wt_ph8_3 wt_ph8_1 wt_ph8_2 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 +TR24|c0_g1_i1 0.106533882165825 -0.313797916782532 0.025003996669227 1.39963914188743 1.22079106142351 1.25695072471892 -1.19180739240392 -1.23133575659056 -1.2719777410879 +TR2779|c0_g1_i1 -0.795433018475884 -1.23380302158535 -0.574143153586594 1.74646076035339 1.75438767612502 1.74380874666379 -1.13287411273457 -0.795433018475884 -0.712970858283911 +TR3091|c0_g1_i1 -2.42438780178849 -2.77802475640319 -2.62602166295814 1.43575453462855 1.4783149968566 1.36038927229391 1.02359379610527 1.32351327005887 1.20686835120661 +TR131|c0_g1_i1 -3.50802026981862 -3.6944333940495 -3.55241438917708 1.98577454287534 1.99158406095747 1.95736061514986 1.41625240401813 1.71671228997234 1.68718414007205 +TR5075|c0_g1_i1 -1.04544737992556 -0.329240345926152 -0.393370683345868 2.50474970263492 2.07793503557972 2.30706903479522 -2.04544737992556 -1.68287730054085 -1.39337068334587 +TR3788|c0_g1_i1 -1.22775484082629 -0.443483531881724 -0.874117886211586 -0.353285722910146 -0.874117886211586 -0.590324920210995 1.12588211378841 1.65760259323259 1.57960008123132
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/define_clusters_by_cutting_tree/subcluster_2_log2_medianCentered_fpkm.matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +wt_37_2 wt_37_3 wt_37_1 wt_ph8_3 wt_ph8_1 wt_ph8_2 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 +TR4277|c0_g1_i1 3.24415794782388 3.31812623217364 3.18414689752048 -1.44630436384266 -1.5322044372483 -1.46308007659348 -1.98611482817144 -1.80411699442855 -1.51461037723356 +TR2672|c0_g1_i1 0.965440325233136 1.96544032523314 1.58211168568163 0.965440325233136 -0.619522175488021 0.0585497296246169 -2.94145027037538 -0.619522175488021 -1.35648776965423 +TR127|c1_g1_i1 1.25755965737847 2.52059406321227 2.02309440374145 -0.0643684375088904 -1.06436843750889 -1.06436843750889 -0.479405936787734 -2.06436843750889 -1.06436843750889 +TR2107|c1_g1_i1 2.49178842221691 2.62929194596684 2.16986032732955 -1.41510217339161 -2.41510217339161 -1.83013967267045 -0.607747251334006 -0.607747251334006 -0.41510217339161 +TR5055|c0_g2_i1 1.90528891290538 0.865760548718745 1.50319046933404 -0.982236357836205 -0.982236357836205 0.280798047997588 -0.982236357836205 -0.304164452723568 -1.30416445272357 +TR4761|c0_g1_i1 2.06406810079911 1.80544476674762 1.90822498634624 -0.339510283104669 -0.357888812419525 -0.296334141902888 -1.67981690730689 -1.51400801433681 -1.59017969482221 +TR1894|c2_g1_i1 2.11263053903627 1.56008951600749 1.23816142112012 -1.34680107960103 -0.346801079601032 -1.34680107960103 -1.34680107960103 -0.761838578879876 0.238161421120124
--- /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 Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +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 4.57661492404411 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 5.71221669652109 5.72452884931028 -0.0104554076697487 0.738553450989727 -0.0141566025529196 0.988705042660126 0.988705042660126
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 03:12:34 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 03:12:34 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,38 @@ +wt_37_1 wt_37_2 wt_37_3 wt_GSNO_1 wt_GSNO_2 wt_GSNO_3 +TR24|c0_g1_i1 85 90 67 35 34 36 +TR2779|c0_g1_i1 217 186 137 186 197 147 +TR127|c1_g1_i1 16 9 23 0 1 2 +TR2107|c1_g1_i1 47 59 65 6 7 6 +TR2011|c5_g1_i1 4 11 4 5 7 8 +TR4163|c0_g1_i1 425 368 422 216 210 172 +TR5055|c0_g2_i1 27 36 17 7 3 4 +TR1449|c0_g1_i1 207 196 230 113 91 66 +TR1982|c2_g1_i1 6 7 7 3 8 4 +TR1492|c0_g1_i2 1921 1895 1906 1263 1319 1104 +TR1122|c0_g1_i1 0 2 3 0 0 3 +TR2278|c0_g1_i1 598 497 610 406 413 333 +TR4084|c0_g1_i1 86 95 148 111 127 77 +TR4761|c0_g1_i1 1875 2089 1746 174 165 155 +TR3638|c0_g1_i1 712 647 676 184 174 117 +TR3854|c0_g1_i1 1864 1878 1734 2173 2151 1775 +TR131|c0_g1_i1 31 32 28 1233 1208 1001 +TR5075|c0_g1_i1 21 13 22 8 10 6 +TR2182|c3_g2_i6 4 1 3 0 0 3 +TR3788|c0_g1_i1 22 17 30 132 125 91 +TR4859|c0_g1_i1 8 6 12 1 3 4 +TR2487|c0_g1_i1 424 386 383 866 806 689 +TR2122|c0_g2_i2 136 145 135 157 201 155 +TR4277|c0_g1_i1 4284 4466 4701 134 164 118 +TR4669|c0_g2_i1 0 0 0 0 218 209 +TR3091|c0_g1_i1 19 22 17 308 284 250 +TR3807|c0_g1_i1 2 6 4 0 1 0 +TR1894|c2_g1_i1 11 21 14 2 5 1 +TR5212|c0_g1_i1 78 64 89 98 108 73 +TR939|c0_g1_i1 99 96 99 89 88 72 +TR1891|c0_g1_i1 124 115 138 139 111 97 +TR2672|c0_g1_i1 22 14 29 4 2 0 +TR2844|c0_g1_i1 178 166 211 214 223 161 +TR1837|c2_g1_i1 0 1 0 1 4 1 +TR1678|c0_g1_i1 1 1 0 0 2 0 +TR3249|c0_g1_i1 1 1 2 1 0 4 +TR1479|c0_g1_i1 141 136 178 324 354 277
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,38 @@ +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.count_matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,38 @@ +wt_37_1 wt_37_2 wt_37_3 wt_GSNO_1 wt_GSNO_2 wt_GSNO_3 +TR24|c0_g1_i1 85 90 67 35 34 36 +TR2779|c0_g1_i1 217 186 137 186 197 147 +TR127|c1_g1_i1 16 9 23 0 1 2 +TR2107|c1_g1_i1 47 59 65 6 7 6 +TR2011|c5_g1_i1 4 11 4 5 7 8 +TR4163|c0_g1_i1 425 368 422 216 210 172 +TR5055|c0_g2_i1 27 36 17 7 3 4 +TR1449|c0_g1_i1 207 196 230 113 91 66 +TR1982|c2_g1_i1 6 7 7 3 8 4 +TR1492|c0_g1_i2 1921 1895 1906 1263 1319 1104 +TR1122|c0_g1_i1 0 2 3 0 0 3 +TR2278|c0_g1_i1 598 497 610 406 413 333 +TR4084|c0_g1_i1 86 95 148 111 127 77 +TR4761|c0_g1_i1 1875 2089 1746 174 165 155 +TR3638|c0_g1_i1 712 647 676 184 174 117 +TR3854|c0_g1_i1 1864 1878 1734 2173 2151 1775 +TR131|c0_g1_i1 31 32 28 1233 1208 1001 +TR5075|c0_g1_i1 21 13 22 8 10 6 +TR2182|c3_g2_i6 4 1 3 0 0 3 +TR3788|c0_g1_i1 22 17 30 132 125 91 +TR4859|c0_g1_i1 8 6 12 1 3 4 +TR2487|c0_g1_i1 424 386 383 866 806 689 +TR2122|c0_g2_i2 136 145 135 157 201 155 +TR4277|c0_g1_i1 4284 4466 4701 134 164 118 +TR4669|c0_g2_i1 0 0 0 0 218 209 +TR3091|c0_g1_i1 19 22 17 308 284 250 +TR3807|c0_g1_i1 2 6 4 0 1 0 +TR1894|c2_g1_i1 11 21 14 2 5 1 +TR5212|c0_g1_i1 78 64 89 98 108 73 +TR939|c0_g1_i1 99 96 99 89 88 72 +TR1891|c0_g1_i1 124 115 138 139 111 97 +TR2672|c0_g1_i1 22 14 29 4 2 0 +TR2844|c0_g1_i1 178 166 211 214 223 161 +TR1837|c2_g1_i1 0 1 0 1 4 1 +TR1678|c0_g1_i1 1 1 0 0 2 0 +TR3249|c0_g1_i1 1 1 2 1 0 4 +TR1479|c0_g1_i1 141 136 178 324 354 277
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,38 @@ +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.count_matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,38 @@ +wt_37_1 wt_37_2 wt_37_3 wt_GSNO_1 wt_GSNO_2 wt_GSNO_3 +TR24|c0_g1_i1 85 90 67 35 34 36 +TR2779|c0_g1_i1 217 186 137 186 197 147 +TR127|c1_g1_i1 16 9 23 0 1 2 +TR2107|c1_g1_i1 47 59 65 6 7 6 +TR2011|c5_g1_i1 4 11 4 5 7 8 +TR4163|c0_g1_i1 425 368 422 216 210 172 +TR5055|c0_g2_i1 27 36 17 7 3 4 +TR1449|c0_g1_i1 207 196 230 113 91 66 +TR1982|c2_g1_i1 6 7 7 3 8 4 +TR1492|c0_g1_i2 1921 1895 1906 1263 1319 1104 +TR1122|c0_g1_i1 0 2 3 0 0 3 +TR2278|c0_g1_i1 598 497 610 406 413 333 +TR4084|c0_g1_i1 86 95 148 111 127 77 +TR4761|c0_g1_i1 1875 2089 1746 174 165 155 +TR3638|c0_g1_i1 712 647 676 184 174 117 +TR3854|c0_g1_i1 1864 1878 1734 2173 2151 1775 +TR131|c0_g1_i1 31 32 28 1233 1208 1001 +TR5075|c0_g1_i1 21 13 22 8 10 6 +TR2182|c3_g2_i6 4 1 3 0 0 3 +TR3788|c0_g1_i1 22 17 30 132 125 91 +TR4859|c0_g1_i1 8 6 12 1 3 4 +TR2487|c0_g1_i1 424 386 383 866 806 689 +TR2122|c0_g2_i2 136 145 135 157 201 155 +TR4277|c0_g1_i1 4284 4466 4701 134 164 118 +TR4669|c0_g2_i1 0 0 0 0 218 209 +TR3091|c0_g1_i1 19 22 17 308 284 250 +TR3807|c0_g1_i1 2 6 4 0 1 0 +TR1894|c2_g1_i1 11 21 14 2 5 1 +TR5212|c0_g1_i1 78 64 89 98 108 73 +TR939|c0_g1_i1 99 96 99 89 88 72 +TR1891|c0_g1_i1 124 115 138 139 111 97 +TR2672|c0_g1_i1 22 14 29 4 2 0 +TR2844|c0_g1_i1 178 166 211 214 223 161 +TR1837|c2_g1_i1 0 1 0 1 4 1 +TR1678|c0_g1_i1 1 1 0 0 2 0 +TR3249|c0_g1_i1 1 1 2 1 0 4 +TR1479|c0_g1_i1 141 136 178 324 354 277
--- /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 Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +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 4.85332629705957 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
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset Thu Jun 14 03:12:34 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 03:12:34 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,39 @@ +wt_37_1 wt_37_2 wt_37_3 wt_ph8_1 wt_ph8_2 wt_ph8_3 +TR24|c0_g1_i1 85 90 67 196 201 222 +TR2779|c0_g1_i1 217 186 137 1094 1086 1088 +TR127|c1_g1_i1 16 9 23 1 1 3 +TR2107|c1_g1_i1 47 59 65 1 2 3 +TR2011|c5_g1_i1 4 11 4 4 8 3 +TR4163|c0_g1_i1 425 368 422 254 212 234 +TR5055|c0_g2_i1 27 36 17 4 11 4 +TR1449|c0_g1_i1 207 196 230 130 107 124 +TR1982|c2_g1_i1 6 7 7 9 11 16 +TR1859|c3_g1_i1 1 0 0 2 4 1 +TR1492|c0_g1_i2 1921 1895 1906 929 922 899 +TR1122|c0_g1_i1 0 2 3 1 0 1 +TR2278|c0_g1_i1 598 497 610 409 337 323 +TR4084|c0_g1_i1 86 95 148 201 158 175 +TR4761|c0_g1_i1 1875 2089 1746 389 406 394 +TR3638|c0_g1_i1 712 647 676 344 338 324 +TR2090|c0_g1_i1 0 0 0 0 9 10 +TR3854|c0_g1_i1 1864 1878 1734 2142 2155 2216 +TR131|c0_g1_i1 31 32 28 1492 1457 1486 +TR5075|c0_g1_i1 21 13 22 121 142 163 +TR2182|c3_g2_i6 4 1 3 2 3 1 +TR3788|c0_g1_i1 22 17 30 22 27 32 +TR4859|c0_g1_i1 8 6 12 1 2 1 +TR2487|c0_g1_i1 424 386 383 989 1032 963 +TR2122|c0_g2_i2 136 145 135 398 344 369 +TR4277|c0_g1_i1 4284 4466 4701 162 170 172 +TR3091|c0_g1_i1 19 22 17 343 316 333 +TR3807|c0_g1_i1 2 6 4 1 0 0 +TR1894|c2_g1_i1 11 21 14 3 1 1 +TR5212|c0_g1_i1 78 64 89 105 84 103 +TR939|c0_g1_i1 99 96 99 103 108 107 +TR1891|c0_g1_i1 124 115 138 411 384 365 +TR2672|c0_g1_i1 22 14 29 4 7 14 +TR2844|c0_g1_i1 178 166 211 245 213 199 +TR1837|c2_g1_i1 0 1 0 3 2 0 +TR1678|c0_g1_i1 1 1 0 10 6 8 +TR3249|c0_g1_i1 1 1 2 1 7 6 +TR1479|c0_g1_i1 141 136 178 363 302 367
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,39 @@ +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.count_matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,39 @@ +wt_37_1 wt_37_2 wt_37_3 wt_ph8_1 wt_ph8_2 wt_ph8_3 +TR24|c0_g1_i1 85 90 67 196 201 222 +TR2779|c0_g1_i1 217 186 137 1094 1086 1088 +TR127|c1_g1_i1 16 9 23 1 1 3 +TR2107|c1_g1_i1 47 59 65 1 2 3 +TR2011|c5_g1_i1 4 11 4 4 8 3 +TR4163|c0_g1_i1 425 368 422 254 212 234 +TR5055|c0_g2_i1 27 36 17 4 11 4 +TR1449|c0_g1_i1 207 196 230 130 107 124 +TR1982|c2_g1_i1 6 7 7 9 11 16 +TR1859|c3_g1_i1 1 0 0 2 4 1 +TR1492|c0_g1_i2 1921 1895 1906 929 922 899 +TR1122|c0_g1_i1 0 2 3 1 0 1 +TR2278|c0_g1_i1 598 497 610 409 337 323 +TR4084|c0_g1_i1 86 95 148 201 158 175 +TR4761|c0_g1_i1 1875 2089 1746 389 406 394 +TR3638|c0_g1_i1 712 647 676 344 338 324 +TR2090|c0_g1_i1 0 0 0 0 9 10 +TR3854|c0_g1_i1 1864 1878 1734 2142 2155 2216 +TR131|c0_g1_i1 31 32 28 1492 1457 1486 +TR5075|c0_g1_i1 21 13 22 121 142 163 +TR2182|c3_g2_i6 4 1 3 2 3 1 +TR3788|c0_g1_i1 22 17 30 22 27 32 +TR4859|c0_g1_i1 8 6 12 1 2 1 +TR2487|c0_g1_i1 424 386 383 989 1032 963 +TR2122|c0_g2_i2 136 145 135 398 344 369 +TR4277|c0_g1_i1 4284 4466 4701 162 170 172 +TR3091|c0_g1_i1 19 22 17 343 316 333 +TR3807|c0_g1_i1 2 6 4 1 0 0 +TR1894|c2_g1_i1 11 21 14 3 1 1 +TR5212|c0_g1_i1 78 64 89 105 84 103 +TR939|c0_g1_i1 99 96 99 103 108 107 +TR1891|c0_g1_i1 124 115 138 411 384 365 +TR2672|c0_g1_i1 22 14 29 4 7 14 +TR2844|c0_g1_i1 178 166 211 245 213 199 +TR1837|c2_g1_i1 0 1 0 3 2 0 +TR1678|c0_g1_i1 1 1 0 10 6 8 +TR3249|c0_g1_i1 1 1 2 1 7 6 +TR1479|c0_g1_i1 141 136 178 363 302 367
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,39 @@ +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.count_matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,39 @@ +wt_37_1 wt_37_2 wt_37_3 wt_ph8_1 wt_ph8_2 wt_ph8_3 +TR24|c0_g1_i1 85 90 67 196 201 222 +TR2779|c0_g1_i1 217 186 137 1094 1086 1088 +TR127|c1_g1_i1 16 9 23 1 1 3 +TR2107|c1_g1_i1 47 59 65 1 2 3 +TR2011|c5_g1_i1 4 11 4 4 8 3 +TR4163|c0_g1_i1 425 368 422 254 212 234 +TR5055|c0_g2_i1 27 36 17 4 11 4 +TR1449|c0_g1_i1 207 196 230 130 107 124 +TR1982|c2_g1_i1 6 7 7 9 11 16 +TR1859|c3_g1_i1 1 0 0 2 4 1 +TR1492|c0_g1_i2 1921 1895 1906 929 922 899 +TR1122|c0_g1_i1 0 2 3 1 0 1 +TR2278|c0_g1_i1 598 497 610 409 337 323 +TR4084|c0_g1_i1 86 95 148 201 158 175 +TR4761|c0_g1_i1 1875 2089 1746 389 406 394 +TR3638|c0_g1_i1 712 647 676 344 338 324 +TR2090|c0_g1_i1 0 0 0 0 9 10 +TR3854|c0_g1_i1 1864 1878 1734 2142 2155 2216 +TR131|c0_g1_i1 31 32 28 1492 1457 1486 +TR5075|c0_g1_i1 21 13 22 121 142 163 +TR2182|c3_g2_i6 4 1 3 2 3 1 +TR3788|c0_g1_i1 22 17 30 22 27 32 +TR4859|c0_g1_i1 8 6 12 1 2 1 +TR2487|c0_g1_i1 424 386 383 989 1032 963 +TR2122|c0_g2_i2 136 145 135 398 344 369 +TR4277|c0_g1_i1 4284 4466 4701 162 170 172 +TR3091|c0_g1_i1 19 22 17 343 316 333 +TR3807|c0_g1_i1 2 6 4 1 0 0 +TR1894|c2_g1_i1 11 21 14 3 1 1 +TR5212|c0_g1_i1 78 64 89 105 84 103 +TR939|c0_g1_i1 99 96 99 103 108 107 +TR1891|c0_g1_i1 124 115 138 411 384 365 +TR2672|c0_g1_i1 22 14 29 4 7 14 +TR2844|c0_g1_i1 178 166 211 245 213 199 +TR1837|c2_g1_i1 0 1 0 3 2 0 +TR1678|c0_g1_i1 1 1 0 10 6 8 +TR3249|c0_g1_i1 1 1 2 1 7 6 +TR1479|c0_g1_i1 141 136 178 363 302 367
--- /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 Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +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 -2.30255444666643 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 03:12:34 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 03:12:34 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,40 @@ +wt_GSNO_1 wt_GSNO_2 wt_GSNO_3 wt_ph8_1 wt_ph8_2 wt_ph8_3 +TR24|c0_g1_i1 35 34 36 196 201 222 +TR2779|c0_g1_i1 186 197 147 1094 1086 1088 +TR127|c1_g1_i1 0 1 2 1 1 3 +TR2107|c1_g1_i1 6 7 6 1 2 3 +TR2011|c5_g1_i1 5 7 8 4 8 3 +TR4163|c0_g1_i1 216 210 172 254 212 234 +TR5055|c0_g2_i1 7 3 4 4 11 4 +TR1449|c0_g1_i1 113 91 66 130 107 124 +TR1982|c2_g1_i1 3 8 4 9 11 16 +TR1859|c3_g1_i1 0 0 0 2 4 1 +TR1492|c0_g1_i2 1263 1319 1104 929 922 899 +TR1122|c0_g1_i1 0 0 3 1 0 1 +TR2278|c0_g1_i1 406 413 333 409 337 323 +TR4084|c0_g1_i1 111 127 77 201 158 175 +TR4761|c0_g1_i1 174 165 155 389 406 394 +TR3638|c0_g1_i1 184 174 117 344 338 324 +TR2090|c0_g1_i1 0 0 22 0 9 10 +TR3854|c0_g1_i1 2173 2151 1775 2142 2155 2216 +TR131|c0_g1_i1 1233 1208 1001 1492 1457 1486 +TR5075|c0_g1_i1 8 10 6 121 142 163 +TR2182|c3_g2_i6 0 0 3 2 3 1 +TR3788|c0_g1_i1 132 125 91 22 27 32 +TR4859|c0_g1_i1 1 3 4 1 2 1 +TR2487|c0_g1_i1 866 806 689 989 1032 963 +TR2122|c0_g2_i2 157 201 155 398 344 369 +TR4277|c0_g1_i1 134 164 118 162 170 172 +TR4669|c0_g2_i1 0 218 209 0 0 0 +TR3091|c0_g1_i1 308 284 250 343 316 333 +TR3807|c0_g1_i1 0 1 0 1 0 0 +TR1894|c2_g1_i1 2 5 1 3 1 1 +TR5212|c0_g1_i1 98 108 73 105 84 103 +TR939|c0_g1_i1 89 88 72 103 108 107 +TR1891|c0_g1_i1 139 111 97 411 384 365 +TR2672|c0_g1_i1 4 2 0 4 7 14 +TR2844|c0_g1_i1 214 223 161 245 213 199 +TR1837|c2_g1_i1 1 4 1 3 2 0 +TR1678|c0_g1_i1 0 2 0 10 6 8 +TR3249|c0_g1_i1 1 0 4 1 7 6 +TR1479|c0_g1_i1 324 354 277 363 302 367
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,40 @@ +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.count_matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,40 @@ +wt_GSNO_1 wt_GSNO_2 wt_GSNO_3 wt_ph8_1 wt_ph8_2 wt_ph8_3 +TR24|c0_g1_i1 35 34 36 196 201 222 +TR2779|c0_g1_i1 186 197 147 1094 1086 1088 +TR127|c1_g1_i1 0 1 2 1 1 3 +TR2107|c1_g1_i1 6 7 6 1 2 3 +TR2011|c5_g1_i1 5 7 8 4 8 3 +TR4163|c0_g1_i1 216 210 172 254 212 234 +TR5055|c0_g2_i1 7 3 4 4 11 4 +TR1449|c0_g1_i1 113 91 66 130 107 124 +TR1982|c2_g1_i1 3 8 4 9 11 16 +TR1859|c3_g1_i1 0 0 0 2 4 1 +TR1492|c0_g1_i2 1263 1319 1104 929 922 899 +TR1122|c0_g1_i1 0 0 3 1 0 1 +TR2278|c0_g1_i1 406 413 333 409 337 323 +TR4084|c0_g1_i1 111 127 77 201 158 175 +TR4761|c0_g1_i1 174 165 155 389 406 394 +TR3638|c0_g1_i1 184 174 117 344 338 324 +TR2090|c0_g1_i1 0 0 22 0 9 10 +TR3854|c0_g1_i1 2173 2151 1775 2142 2155 2216 +TR131|c0_g1_i1 1233 1208 1001 1492 1457 1486 +TR5075|c0_g1_i1 8 10 6 121 142 163 +TR2182|c3_g2_i6 0 0 3 2 3 1 +TR3788|c0_g1_i1 132 125 91 22 27 32 +TR4859|c0_g1_i1 1 3 4 1 2 1 +TR2487|c0_g1_i1 866 806 689 989 1032 963 +TR2122|c0_g2_i2 157 201 155 398 344 369 +TR4277|c0_g1_i1 134 164 118 162 170 172 +TR4669|c0_g2_i1 0 218 209 0 0 0 +TR3091|c0_g1_i1 308 284 250 343 316 333 +TR3807|c0_g1_i1 0 1 0 1 0 0 +TR1894|c2_g1_i1 2 5 1 3 1 1 +TR5212|c0_g1_i1 98 108 73 105 84 103 +TR939|c0_g1_i1 89 88 72 103 108 107 +TR1891|c0_g1_i1 139 111 97 411 384 365 +TR2672|c0_g1_i1 4 2 0 4 7 14 +TR2844|c0_g1_i1 214 223 161 245 213 199 +TR1837|c2_g1_i1 1 4 1 3 2 0 +TR1678|c0_g1_i1 0 2 0 10 6 8 +TR3249|c0_g1_i1 1 0 4 1 7 6 +TR1479|c0_g1_i1 324 354 277 363 302 367
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,40 @@ +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.count_matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,40 @@ +wt_GSNO_1 wt_GSNO_2 wt_GSNO_3 wt_ph8_1 wt_ph8_2 wt_ph8_3 +TR24|c0_g1_i1 35 34 36 196 201 222 +TR2779|c0_g1_i1 186 197 147 1094 1086 1088 +TR127|c1_g1_i1 0 1 2 1 1 3 +TR2107|c1_g1_i1 6 7 6 1 2 3 +TR2011|c5_g1_i1 5 7 8 4 8 3 +TR4163|c0_g1_i1 216 210 172 254 212 234 +TR5055|c0_g2_i1 7 3 4 4 11 4 +TR1449|c0_g1_i1 113 91 66 130 107 124 +TR1982|c2_g1_i1 3 8 4 9 11 16 +TR1859|c3_g1_i1 0 0 0 2 4 1 +TR1492|c0_g1_i2 1263 1319 1104 929 922 899 +TR1122|c0_g1_i1 0 0 3 1 0 1 +TR2278|c0_g1_i1 406 413 333 409 337 323 +TR4084|c0_g1_i1 111 127 77 201 158 175 +TR4761|c0_g1_i1 174 165 155 389 406 394 +TR3638|c0_g1_i1 184 174 117 344 338 324 +TR2090|c0_g1_i1 0 0 22 0 9 10 +TR3854|c0_g1_i1 2173 2151 1775 2142 2155 2216 +TR131|c0_g1_i1 1233 1208 1001 1492 1457 1486 +TR5075|c0_g1_i1 8 10 6 121 142 163 +TR2182|c3_g2_i6 0 0 3 2 3 1 +TR3788|c0_g1_i1 132 125 91 22 27 32 +TR4859|c0_g1_i1 1 3 4 1 2 1 +TR2487|c0_g1_i1 866 806 689 989 1032 963 +TR2122|c0_g2_i2 157 201 155 398 344 369 +TR4277|c0_g1_i1 134 164 118 162 170 172 +TR4669|c0_g2_i1 0 218 209 0 0 0 +TR3091|c0_g1_i1 308 284 250 343 316 333 +TR3807|c0_g1_i1 0 1 0 1 0 0 +TR1894|c2_g1_i1 2 5 1 3 1 1 +TR5212|c0_g1_i1 98 108 73 105 84 103 +TR939|c0_g1_i1 89 88 72 103 108 107 +TR1891|c0_g1_i1 139 111 97 411 384 365 +TR2672|c0_g1_i1 4 2 0 4 7 14 +TR2844|c0_g1_i1 214 223 161 245 213 199 +TR1837|c2_g1_i1 1 4 1 3 2 0 +TR1678|c0_g1_i1 0 2 0 10 6 8 +TR3249|c0_g1_i1 1 0 4 1 7 6 +TR1479|c0_g1_i1 324 354 277 363 302 367
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/express_bowtie/results.xprs Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm +1 TRINITY_DN2_c3_g1_i1 202 0.000000 0 0 0.000000 0.000000 0.000000e00 0.000000e00 0.000000e00 0.000000e00 0.000000e00 F 0.000000e+00 +2 TRINITY_DN1_c0_g1_i1 380 109.247050 5 5 5.000000 17.391774 0.000000e00 0.000000e00 4.160711e06 4.160711e06 4.160711e06 T 6.610131e+05 +3 TRINITY_DN2_c0_g1_i1 279 0.000000 0 0 0.000000 0.000000 0.000000e00 0.000000e00 0.000000e00 0.000000e00 0.000000e00 F 0.000000e+00 +4 TRINITY_DN0_c0_g1_i1 229 0.000000 0 0 0.000000 0.000000 0.000000e00 0.000000e00 0.000000e00 0.000000e00 0.000000e00 F 0.000000e+00 +5 TRINITY_DN2_c1_g1_i1 541 259.008053 5 5 5.000000 10.443691 0.000000e00 0.000000e00 1.754947e06 1.754947e06 1.754947e06 T 2.788088e+05 +6 TRINITY_DN2_c2_g1_i1 240 240.000000 1 1 1.000000 1.000000 0.000000e00 0.000000e00 3.787879e05 3.787879e05 3.787879e05 T 6.017811e+04 +7 TRINITY_DN3_c0_g1_i1 216 0.000000 0 0 0.000000 0.000000 0.000000e00 0.000000e00 0.000000e00 0.000000e00 0.000000e00 F 0.000000e+00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/express_bowtie/results_B.xprs Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm +1 TRINITY_DN0_c0_g1_i1 380 109.247050 5 5 5.000000 17.391774 0.000000e+00 0.000000e+00 4.160711e+06 4.160711e+06 4.160711e+06 T 6.610131e+05 +2 TRINITY_DN2_c0_g1_i1 279 0.000000 0 0 0.000000 0.000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 F 0.000000e+00 +3 TRINITY_DN2_c1_g1_i1 240 240.000000 1 1 1.000000 1.000000 0.000000e+00 0.000000e+00 3.787879e+05 3.787879e+05 3.787879e+05 T 6.017811e+04 +4 TRINITY_DN1_c0_g1_i1 229 0.000000 0 0 0.000000 0.000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 F 0.000000e+00 +5 TRINITY_DN3_c0_g1_i1 216 0.000000 0 0 0.000000 0.000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 F 0.000000e+00 +6 TRINITY_DN2_c3_g1_i1 202 0.000000 0 0 0.000000 0.000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 F 0.000000e+00 +7 TRINITY_DN2_c2_g1_i1 541 259.008053 5 5 5.000000 10.443691 0.000000e+00 0.000000e+00 1.754947e+06 1.754947e+06 1.754947e+06 T 2.788088e+05
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/express_bowtie/sample_A Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm +NA TRINITY_DN3_c0_g1 216.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN2_c2_g1 240.00 240.00 NA NA NA 1.00 NA NA 378787.90 NA NA NA 60178.11 +NA TRINITY_DN2_c3_g1 202.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN0_c0_g1 229.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN2_c0_g1 279.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN1_c0_g1 380.00 109.25 NA NA NA 17.39 NA NA 4160711.00 NA NA NA 661013.1 +NA TRINITY_DN2_c1_g1 541.00 259.01 NA NA NA 10.44 NA NA 1754947.00 NA NA NA 278808.8
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/express_bowtie/sample_B Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm +NA TRINITY_DN3_c0_g1 216.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN2_c1_g1 240.00 240.00 NA NA NA 1.00 NA NA 378787.90 NA NA NA 60178.11 +NA TRINITY_DN2_c3_g1 202.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN0_c0_g1 380.00 109.25 NA NA NA 17.39 NA NA 4160711.00 NA NA NA 661013.1 +NA TRINITY_DN1_c0_g1 229.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN2_c0_g1 279.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN2_c2_g1 541.00 259.01 NA NA NA 10.44 NA NA 1754947.00 NA NA NA 278808.8
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/kallisto/abundance.tsv Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +target_id length eff_length est_counts tpm +TRINITY_DN1_c0_g1_i1 380 133.091 13 114025 +TRINITY_DN0_c0_g1_i1 229 31.75 7 257370 +TRINITY_DN2_c0_g1_i1 279 55.7143 1 20952.6 +TRINITY_DN2_c1_g1_i1 541 279.667 15 62611.6 +TRINITY_DN2_c2_g1_i1 240 42.75 4 109227 +TRINITY_DN2_c3_g1_i1 202 19 0 0 +TRINITY_DN3_c0_g1_i1 216 18.75 7 435814
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/kallisto/abundance.tsv.genes Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +target_id length eff_length est_counts tpm +TRINITY_DN3_c0_g1 216.00 18.75 7.00 435814.00 +TRINITY_DN2_c2_g1 240.00 42.75 4.00 109227.00 +TRINITY_DN2_c3_g1 202.00 19.00 0.00 0.00 +TRINITY_DN0_c0_g1 229.00 31.75 7.00 257370.00 +TRINITY_DN2_c0_g1 279.00 55.71 1.00 20952.60 +TRINITY_DN1_c0_g1 380.00 133.09 13.00 114025.00 +TRINITY_DN2_c1_g1 541.00 279.67 15.00 62611.60
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/kallisto/abundance_B.tsv Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +target_id length eff_length est_counts tpm +TRINITY_DN1_c0_g1_i1 229 31.75 7 257370 +TRINITY_DN0_c0_g1_i1 380 133.091 13 114025 +TRINITY_DN2_c0_g1_i1 279 55.7143 1 20952.6 +TRINITY_DN2_c2_g1_i1 541 279.667 15 62611.6 +TRINITY_DN2_c1_g1_i1 240 42.75 4 109227 +TRINITY_DN2_c3_g1_i1 202 19 0 0 +TRINITY_DN3_c0_g1_i1 216 18.75 7 435814
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/kallisto/abundance_B.tsv.genes Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +target_id length eff_length est_counts tpm +TRINITY_DN3_c0_g1 216.00 18.75 7.00 435814.00 +TRINITY_DN2_c1_g1 240.00 42.75 4.00 109227.00 +TRINITY_DN2_c3_g1 202.00 19.00 0.00 0.00 +TRINITY_DN0_c0_g1 380.00 133.09 13.00 114025.00 +TRINITY_DN2_c0_g1 279.00 55.71 1.00 20952.60 +TRINITY_DN1_c0_g1 229.00 31.75 7.00 257370.00 +TRINITY_DN2_c2_g1 541.00 279.67 15.00 62611.60
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_express_bowtie/matrix.TMM.EXPR.matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN2_c1_g1_i1 278808.8 60178.11 +TRINITY_DN1_c0_g1_i1 0 0 +TRINITY_DN2_c2_g1_i1 60178.11 278808.8 +TRINITY_DN2_c0_g1_i1 0 0 +TRINITY_DN3_c0_g1_i1 0 0 +TRINITY_DN2_c3_g1_i1 0 0 +TRINITY_DN0_c0_g1_i1 661013.1 661013.1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_express_bowtie/matrix.TPM.not_cross_norm Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN2_c1_g1_i1 278808.8 60178.11 +TRINITY_DN1_c0_g1_i1 0 0 +TRINITY_DN2_c2_g1_i1 60178.11 278808.8 +TRINITY_DN2_c0_g1_i1 0 0 +TRINITY_DN3_c0_g1_i1 0 0 +TRINITY_DN2_c3_g1_i1 0 0 +TRINITY_DN0_c0_g1_i1 661013.1 661013.1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_express_bowtie/matrix.counts.matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN2_c1_g1_i1 10.443691 1.000000 +TRINITY_DN1_c0_g1_i1 0.000000 0.000000 +TRINITY_DN2_c2_g1_i1 1.000000 10.443691 +TRINITY_DN2_c0_g1_i1 0.000000 0.000000 +TRINITY_DN3_c0_g1_i1 0.000000 0.000000 +TRINITY_DN2_c3_g1_i1 0.000000 0.000000 +TRINITY_DN0_c0_g1_i1 17.391774 17.391774
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie/matrix.TMM.EXPR.matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN3_c0_g1 0 0 +TRINITY_DN4_c0_g1 0 0 +TRINITY_DN0_c0_g1 331152.79 331152.79 +TRINITY_DN2_c0_g1 0 0 +TRINITY_DN3_c2_g1 524034.76 144812.45 +TRINITY_DN3_c1_g1 144812.45 524034.76 +TRINITY_DN3_c3_g1 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie/matrix.TPM.not_cross_norm Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN3_c0_g1 0 0 +TRINITY_DN4_c0_g1 0 0 +TRINITY_DN0_c0_g1 331152.79 331152.79 +TRINITY_DN2_c0_g1 0 0 +TRINITY_DN3_c2_g1 524034.76 144812.45 +TRINITY_DN3_c1_g1 144812.45 524034.76 +TRINITY_DN3_c3_g1 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie/matrix.counts.matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN3_c0_g1 0.00 0.00 +TRINITY_DN4_c0_g1 0.00 0.00 +TRINITY_DN0_c0_g1 5.00 5.00 +TRINITY_DN2_c0_g1 0.00 0.00 +TRINITY_DN3_c2_g1 1.00 5.00 +TRINITY_DN3_c1_g1 5.00 1.00 +TRINITY_DN3_c3_g1 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie2/matrix.TMM.EXPR.matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN3_c0_g1 0 0 +TRINITY_DN2_c2_g1 529174.03 161779.66 +TRINITY_DN2_c3_g1 0 0 +TRINITY_DN0_c0_g1 309046.31 309046.31 +TRINITY_DN2_c0_g1 0 0 +TRINITY_DN1_c0_g1 0 0 +TRINITY_DN2_c1_g1 161779.66 529174.03
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie2/matrix.TPM.not_cross_norm Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN3_c0_g1 0 0 +TRINITY_DN2_c2_g1 529174.03 161779.66 +TRINITY_DN2_c3_g1 0 0 +TRINITY_DN0_c0_g1 309046.31 309046.31 +TRINITY_DN2_c0_g1 0 0 +TRINITY_DN1_c0_g1 0 0 +TRINITY_DN2_c1_g1 161779.66 529174.03
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie2/matrix.counts.matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN3_c0_g1 0.00 0.00 +TRINITY_DN2_c2_g1 1.00 6.00 +TRINITY_DN2_c3_g1 0.00 0.00 +TRINITY_DN0_c0_g1 5.00 5.00 +TRINITY_DN2_c0_g1 0.00 0.00 +TRINITY_DN1_c0_g1 0.00 0.00 +TRINITY_DN2_c1_g1 6.00 1.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN3_c0_g1 0 0 +TRINITY_DN4_c0_g1 0 0 +TRINITY_DN0_c0_g1 331152.79 331152.79 +TRINITY_DN2_c0_g1 0 0 +TRINITY_DN3_c2_g1 524034.76 144812.45 +TRINITY_DN3_c1_g1 144812.45 524034.76 +TRINITY_DN3_c3_g1 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm.upper_quartile_norm.matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +RSEM RSEM.isoforms_B.results +TRINITY_DN3_c2_g1_i1 524034.76 144812.45 +TRINITY_DN4_c0_g1_i1 0 0 +TRINITY_DN3_c3_g1_i1 0 0 +TRINITY_DN3_c1_g1_i1 144812.45 524034.76 +TRINITY_DN2_c0_g1_i1 0 0 +TRINITY_DN3_c0_g1_i1 0 0 +TRINITY_DN0_c0_g1_i1 331152.79 331152.79
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.UpperQuartile.EXPR.matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +sample_A sample_B +TRINITY_DN2_c0_g1 0 0 +TRINITY_DN1_c0_g1 329523.81 329523.81 +TRINITY_DN0_c0_g1 0 0 +TRINITY_DN2_c1_g1 145165.14 525311.05 +TRINITY_DN3_c0_g1 0 0 +TRINITY_DN2_c2_g1 525311.05 145165.14 +TRINITY_DN2_c3_g1 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.counts.matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN3_c0_g1 0.00 0.00 +TRINITY_DN4_c0_g1 0.00 0.00 +TRINITY_DN0_c0_g1 5.00 5.00 +TRINITY_DN2_c0_g1 0.00 0.00 +TRINITY_DN3_c2_g1 1.00 5.00 +TRINITY_DN3_c1_g1 5.00 1.00 +TRINITY_DN3_c3_g1 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie_none/matrix.TPM.not_cross_norm Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN3_c0_g1 0 0 +TRINITY_DN4_c0_g1 0 0 +TRINITY_DN0_c0_g1 331152.79 331152.79 +TRINITY_DN2_c0_g1 0 0 +TRINITY_DN3_c2_g1 524034.76 144812.45 +TRINITY_DN3_c1_g1 144812.45 524034.76 +TRINITY_DN3_c3_g1 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie_none/matrix.counts.matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN3_c0_g1 0.00 0.00 +TRINITY_DN4_c0_g1 0.00 0.00 +TRINITY_DN0_c0_g1 5.00 5.00 +TRINITY_DN2_c0_g1 0.00 0.00 +TRINITY_DN3_c2_g1 1.00 5.00 +TRINITY_DN3_c1_g1 5.00 1.00 +TRINITY_DN3_c3_g1 0.00 0.00
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/count/qcheck/matrix.counts.matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,41 @@ + wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR24|c0_g1_i1 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00 +TR2779|c0_g1_i1 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00 +TR127|c1_g1_i1 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 +TR2107|c1_g1_i1 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00 +TR2011|c5_g1_i1 11.00 4.00 4.00 8.00 5.00 7.00 3.00 4.00 8.00 +TR4163|c0_g1_i1 368.00 422.00 425.00 172.00 216.00 210.00 234.00 254.00 212.00 +TR5055|c0_g2_i1 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00 +TR1449|c0_g1_i1 196.00 230.00 207.00 66.00 113.00 91.00 124.00 130.00 107.00 +TR1982|c2_g1_i1 7.00 7.00 6.00 4.00 3.00 8.00 16.00 9.00 11.00 +TR1859|c3_g1_i1 0.00 0.00 1.00 0.00 0.00 0.00 1.00 2.00 4.00 +TR1492|c0_g1_i2 1895.00 1906.00 1921.00 1104.00 1263.00 1319.00 899.00 929.00 922.00 +TR1122|c0_g1_i1 2.00 3.00 0.00 3.00 0.00 0.00 1.00 1.00 0.00 +TR2278|c0_g1_i1 497.00 610.00 598.00 333.00 406.00 413.00 323.00 409.00 337.00 +TR4084|c0_g1_i1 95.00 148.00 86.00 77.00 111.00 127.00 175.00 201.00 158.00 +TR4761|c0_g1_i1 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00 +TR3638|c0_g1_i1 647.00 676.00 712.00 117.00 184.00 174.00 324.00 344.00 338.00 +TR2090|c0_g1_i1 0.00 0.00 0.00 22.00 0.00 0.02 10.33 0.00 9.09 +TR3854|c0_g1_i1 1878.00 1734.00 1864.00 1775.00 2173.00 2151.00 2216.00 2142.00 2155.00 +TR131|c0_g1_i1 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00 +TR5075|c0_g1_i1 13.00 22.00 21.00 6.00 8.00 10.00 163.00 121.00 142.00 +TR2182|c3_g2_i6 1.44 2.70 3.84 3.35 0.00 0.00 1.22 2.18 2.63 +TR3788|c0_g1_i1 17.00 30.00 22.00 91.00 132.00 125.00 32.00 22.00 27.00 +TR4859|c0_g1_i1 6.00 12.00 8.00 4.00 1.00 3.00 1.00 1.00 2.00 +TR2487|c0_g1_i1 386.00 383.00 424.00 689.00 866.00 806.00 963.00 989.00 1032.00 +TR2122|c0_g2_i2 145.00 135.00 136.00 155.00 157.00 201.00 369.00 398.00 344.00 +TR4277|c0_g1_i1 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00 +TR4669|c0_g2_i1 0.00 0.00 0.00 209.00 0.00 217.50 0.14 0.06 0.18 +TR3091|c0_g1_i1 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00 +TR2130|c1_g3_i1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 +TR3807|c0_g1_i1 6.00 4.00 2.00 0.00 0.00 1.00 0.00 1.00 0.00 +TR1894|c2_g1_i1 21.00 14.00 11.00 1.00 2.00 5.00 1.00 3.00 1.00 +TR5212|c0_g1_i1 64.00 89.00 78.00 73.00 98.00 108.00 103.00 105.00 84.00 +TR939|c0_g1_i1 96.00 99.00 99.00 72.00 89.00 88.00 107.00 103.00 108.00 +TR1891|c0_g1_i1 115.00 137.96 124.00 96.53 139.00 110.94 364.77 411.00 384.00 +TR2672|c0_g1_i1 14.00 29.00 22.00 0.00 4.00 2.00 14.00 4.00 7.00 +TR2844|c0_g1_i1 166.00 211.00 178.00 161.00 214.00 223.00 199.00 245.00 213.00 +TR1837|c2_g1_i1 1.00 0.00 0.00 1.00 1.00 4.00 0.00 3.00 2.00 +TR1678|c0_g1_i1 1.00 0.00 1.00 0.00 0.00 2.00 8.00 10.00 6.00 +TR3249|c0_g1_i1 1.00 2.00 1.00 4.00 1.00 0.00 6.00 1.00 7.00 +TR1479|c0_g1_i1 136.00 178.00 141.00 277.00 324.00 354.00 367.00 363.00 302.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie/RSEM.isoforms.results Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct +TRINITY_DN0_c0_g1_i1 TRINITY_DN0_c0_g1 229 11.55 0.00 0.00 0.00 0.00 +TRINITY_DN1_c0_g1_i1 TRINITY_DN1_c0_g1 380 123.91 5.00 329523.81 3668378.58 100.00 +TRINITY_DN2_c0_g1_i1 TRINITY_DN2_c0_g1 279 35.45 0.00 0.00 0.00 0.00 +TRINITY_DN2_c1_g1_i1 TRINITY_DN2_c1_g1 541 281.27 5.00 145165.14 1616031.03 100.00 +TRINITY_DN2_c2_g1_i1 TRINITY_DN2_c2_g1 240 15.55 1.00 525311.05 5847953.22 100.00 +TRINITY_DN2_c3_g1_i1 TRINITY_DN2_c3_g1 202 3.45 0.00 0.00 0.00 0.00 +TRINITY_DN3_c0_g1_i1 TRINITY_DN3_c0_g1 216 6.82 0.00 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie/RSEM.isoforms_B.results Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct +TRINITY_DN0_c0_g1_i1 TRINITY_DN0_c0_g1 229 11.55 0.00 0.00 0.00 0.00 +TRINITY_DN1_c0_g1_i1 TRINITY_DN1_c0_g1 380 123.91 5.00 329523.81 3668378.58 100.00 +TRINITY_DN2_c0_g1_i1 TRINITY_DN2_c0_g1 279 35.45 0.00 0.00 0.00 0.00 +TRINITY_DN2_c2_g1_i1 TRINITY_DN2_c2_g1 541 281.27 5.00 145165.14 1616031.03 100.00 +TRINITY_DN2_c1_g1_i1 TRINITY_DN2_c1_g1 240 15.55 1.00 525311.05 5847953.22 100.00 +TRINITY_DN2_c3_g1_i1 TRINITY_DN2_c3_g1 202 3.45 0.00 0.00 0.00 0.00 +TRINITY_DN3_c0_g1_i1 TRINITY_DN3_c0_g1 216 6.82 0.00 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie/sample_A Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 11.55 0.00 0.00 0.00 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 123.91 5.00 329523.81 3668378.58 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 35.45 0.00 0.00 0.00 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 541.00 281.27 5.00 145165.14 1616031.03 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 240.00 15.55 1.00 525311.05 5847953.22 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.45 0.00 0.00 0.00 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.82 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie/sample_B Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 11.55 0.00 0.00 0.00 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 123.91 5.00 329523.81 3668378.58 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 35.45 0.00 0.00 0.00 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 541.00 281.27 5.00 145165.14 1616031.03 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 240.00 15.55 1.00 525311.05 5847953.22 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.45 0.00 0.00 0.00 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.82 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie2/RSEM.isoforms.results Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct +TRINITY_DN0_c0_g1_i1 TRINITY_DN0_c0_g1 229 10.58 0.00 0.00 0.00 0.00 +TRINITY_DN1_c0_g1_i1 TRINITY_DN1_c0_g1 380 122.00 5.00 309046.31 3415300.55 100.00 +TRINITY_DN2_c0_g1_i1 TRINITY_DN2_c0_g1 279 32.50 0.00 0.00 0.00 0.00 +TRINITY_DN2_c1_g1_i1 TRINITY_DN2_c1_g1 541 279.67 6.00 161779.66 1787842.67 100.00 +TRINITY_DN2_c2_g1_i1 TRINITY_DN2_c2_g1 240 14.25 1.00 529174.03 5847953.22 100.00 +TRINITY_DN2_c3_g1_i1 TRINITY_DN2_c3_g1 202 3.17 0.00 0.00 0.00 0.00 +TRINITY_DN3_c0_g1_i1 TRINITY_DN3_c0_g1 216 6.25 0.00 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie2/RSEM.isoforms_B.results Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct +TRINITY_DN0_c0_g1_i1 TRINITY_DN0_c0_g1 380 122.00 5.00 309046.31 3415300.55 100.00 +TRINITY_DN1_c0_g1_i1 TRINITY_DN1_c0_g1 229 10.58 0.00 0.00 0.00 0.00 +TRINITY_DN2_c0_g1_i1 TRINITY_DN2_c0_g1 279 32.50 0.00 0.00 0.00 0.00 +TRINITY_DN2_c2_g1_i1 TRINITY_DN2_c2_g1 541 279.67 6.00 161779.66 1787842.67 100.00 +TRINITY_DN2_c1_g1_i1 TRINITY_DN2_c1_g1 240 14.25 1.00 529174.03 5847953.22 100.00 +TRINITY_DN2_c3_g1_i1 TRINITY_DN2_c3_g1 202 3.17 0.00 0.00 0.00 0.00 +TRINITY_DN3_c0_g1_i1 TRINITY_DN3_c0_g1 216 6.25 0.00 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie2/sample_A Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 10.58 0.00 0.00 0.00 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 122.00 5.00 309046.31 3415300.55 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 32.50 0.00 0.00 0.00 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 541.00 279.67 6.00 161779.66 1787842.67 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 240.00 14.25 1.00 529174.03 5847953.22 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.17 0.00 0.00 0.00 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.25 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie2/sample_B Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 380.00 122.00 5.00 309046.31 3415300.55 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 229.00 10.58 0.00 0.00 0.00 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 32.50 0.00 0.00 0.00 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 541.00 279.67 6.00 161779.66 1787842.67 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 240.00 14.25 1.00 529174.03 5847953.22 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.17 0.00 0.00 0.00 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.25 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/salmon/sample_A Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +Name Length EffectiveLength TPM NumReads +TRINITY_DN1_c0_g1_i1 380 120.403 179183 13 +TRINITY_DN0_c0_g1_i1 229 229 55271.5 7.62686 +TRINITY_DN2_c0_g1_i1 279 31.1522 565494 10.6151 +TRINITY_DN2_c1_g1_i1 541 278.129 113370 19 +TRINITY_DN2_c2_g1_i1 240 240 32900.7 4.75801 +TRINITY_DN2_c3_g1_i1 202 202 0 0 +TRINITY_DN3_c0_g1_i1 216 216 53781.8 7
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/salmon/sample_B Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ +Name Length EffectiveLength TPM NumReads +TRINITY_DN2_c2_g1 240.00 240.00 32900.70 4.76 +TRINITY_DN0_c0_g1 229.00 229.00 55271.50 7.63 +TRINITY_DN1_c0_g1 380.00 120.40 179183.00 13.00 +TRINITY_DN2_c0_g1 279.00 31.15 565494.00 10.62 +TRINITY_DN2_c3_g1 202.00 202.00 0.00 0.00 +TRINITY_DN3_c0_g1 216.00 216.00 53781.80 7.00 +TRINITY_DN2_c1_g1 541.00 278.13 113370.00 19.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/samples.txt Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,9 @@ +wt_37 wt_37_1 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_1-SRX707647-SRR1582649_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_1-SRX707647-SRR1582649_2.fastq +wt_37 wt_37_2 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_2-SRX707648-SRR1582650_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_2-SRX707648-SRR1582650_2.fastq +wt_37 wt_37_3 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_3-SRX707649-SRR1582651_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_3-SRX707649-SRR1582651_2.fastq +wt_GSNO wt_GSNO_1 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_1-SRX707644-SRR1582646_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_1-SRX707644-SRR1582646_2.fastq +wt_GSNO wt_GSNO_2 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_2-SRX707645-SRR1582647_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_2-SRX707645-SRR1582647_2.fastq +wt_GSNO wt_GSNO_3 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_3-SRX707646-SRR1582648_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_3-SRX707646-SRR1582648_2.fastq +wt_ph8 wt_ph8_1 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_1-SRX707641-SRR1582643_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_1-SRX707641-SRR1582643_2.fastq +wt_ph8 wt_ph8_2 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_2-SRX707642-SRR1582644_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_2-SRX707642-SRR1582644_2.fastq +wt_ph8 wt_ph8_3 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_3-SRX707643-SRR1582645_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_3-SRX707643-SRR1582645_2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/trinotate/genes.lengths.txt Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,41 @@ +gene_id length +TR24|c0_g1_i1 290.00 +TR2779|c0_g1_i1 186.00 +TR127|c1_g1_i1 229.00 +TR2107|c1_g1_i1 259.00 +TR2011|c5_g1_i1 211.00 +TR4163|c0_g1_i1 368.00 +TR5055|c0_g2_i1 236.00 +TR1449|c0_g1_i1 196.00 +TR1982|c2_g1_i1 227.00 +TR1859|c3_g1_i1 220.00 +TR1492|c0_g1_i2 195.00 +TR1122|c0_g1_i1 222.00 +TR2278|c0_g1_i1 497.00 +TR4084|c0_g1_i1 295.00 +TR4761|c0_g1_i1 289.00 +TR3638|c0_g1_i1 247.00 +TR2090|c0_g1_i1 220.00 +TR3854|c0_g1_i1 178.00 +TR131|c0_g1_i1 232.00 +TR5075|c0_g1_i1 213.00 +TR2182|c3_g2_i6 221.44 +TR3788|c0_g1_i1 217.00 +TR4859|c0_g1_i1 226.00 +TR2487|c0_g1_i1 386.00 +TR2122|c0_g2_i2 145.00 +TR4277|c0_g1_i1 466.00 +TR3091|c0_g1_i1 222.00 +TR2130|c1_g3_i1 220.00 +TR3807|c0_g1_i1 226.00 +TR1894|c2_g1_i1 221.00 +TR5212|c0_g1_i1 264.00 +TR939|c0_g1_i1 296.00 +TR1891|c0_g1_i1 115.00 +TR2672|c0_g1_i1 214.00 +TR2844|c0_g1_i1 166.00 +TR1837|c2_g1_i1 221.00 +TR1678|c0_g1_i1 221.00 +TR3249|c0_g1_i1 221.00 +TR1479|c0_g1_i1 136.00 +TR4669|c0_g2_i1 136.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/trinotate/go_annotations.txt Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,39 @@ +TR24|c0_g1_i1 GO:0003674,GO:0003824,GO:0003865,GO:0005575,GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229,GO:0016491,GO:0016627,GO:0031090,GO:0033765,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0071704,GO:0098588,GO:0098589,GO:1901360 +TR2779|c0_g1_i1 GO:0003674,GO:0003824,GO:0004596,GO:0005575,GO:0005634,GO:0005737,GO:0008080,GO:0016407,GO:0016410,GO:0016740,GO:0016746,GO:0016747,GO:0034212,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464 +TR127|c1_g1_i1 GO:0003674,GO:0003824,GO:0004310,GO:0004311,GO:0004659,GO:0005575,GO:0005789,GO:0006066,GO:0006629,GO:0006694,GO:0006720,GO:0008150,GO:0008152,GO:0008202,GO:0008299,GO:0008610,GO:0009058,GO:0009987,GO:0016020,GO:0016021,GO:0016125,GO:0016126,GO:0016491,GO:0016740,GO:0016765,GO:0031090,GO:0044237,GO:0044238,GO:0044249,GO:0044255,GO:0044281,GO:0044283,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0044711,GO:0044763,GO:0046165,GO:0051996,GO:0071704,GO:0098588,GO:0098589,GO:1901360,GO:1901362,GO:1901576,GO:1901615,GO:1901617 +TR2107|c1_g1_i1 GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175,GO:0004190,GO:0004518,GO:0004519,GO:0005488,GO:0006139,GO:0006259,GO:0006310,GO:0006725,GO:0006807,GO:0008150,GO:0008152,GO:0008233,GO:0009987,GO:0015074,GO:0016740,GO:0016772,GO:0016779,GO:0016787,GO:0016788,GO:0034061,GO:0034641,GO:0043167,GO:0043169,GO:0043170,GO:0044237,GO:0044238,GO:0044260,GO:0046483,GO:0046872,GO:0070001,GO:0070011,GO:0071704,GO:0090304,GO:0097159,GO:1901360,GO:1901363 +TR2011|c5_g1_i1 GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005737,GO:0006801,GO:0006810,GO:0006811,GO:0006812,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169,GO:0044237,GO:0044424,GO:0044464,GO:0044699,GO:0044710,GO:0044765,GO:0046872,GO:0046914,GO:0051234,GO:0055114,GO:0072593 +TR4163|c0_g1_i1 GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005634,GO:0005743,GO:0005829,GO:0006801,GO:0006873,GO:0006875,GO:0006878,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0010035,GO:0010038,GO:0016020,GO:0016530,GO:0016531,GO:0016532,GO:0019725,GO:0019866,GO:0030003,GO:0030234,GO:0031090,GO:0031966,GO:0042221,GO:0042592,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044237,GO:0044422,GO:0044424,GO:0044429,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0044763,GO:0046872,GO:0046914,GO:0046916,GO:0048878,GO:0050801,GO:0050896,GO:0051716,GO:0055065,GO:0055070,GO:0055076,GO:0055080,GO:0055082,GO:0055114,GO:0065007,GO:0065008,GO:0070887,GO:0071241,GO:0071248,GO:0072593 +TR5055|c0_g2_i1 GO:0003674,GO:0005488,GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872,GO:0046914 +TR1449|c0_g1_i1 GO:0003674,GO:0005488,GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872,GO:0046914 +TR1982|c2_g1_i1 GO:0003674,GO:0003824,GO:0003865,GO:0005575,GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229,GO:0016491,GO:0016627,GO:0031090,GO:0033765,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0071704,GO:0098588,GO:0098589,GO:1901360 +TR1859|c3_g1_i1 GO:0003676 +TR1492|c0_g1_i2 GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229 +TR1122|c0_g1_i1 GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234 +TR2278|c0_g1_i1 GO:0031090,GO:0033765 +TR4084|c0_g1_i1 GO:0003674,GO:0005488,GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872,GO:0046914 +TR4761|c0_g1_i1 GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234 +TR3638|c0_g1_i1 GO:0003865,GO:0005575,GO:0005783 +TR2090|c0_g1_i1 GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005634,GO:0005743,GO:0005829,GO:0006801,GO:0006873,GO:0006875,GO:0006878,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0010035,GO:0010038,GO:0016020,GO:0016530,GO:0016531,GO:0016532,GO:0019725,GO:0019866,GO:0030003,GO:0030234,GO:0031090,GO:0031966,GO:0042221,GO:0042592,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044237,GO:0044422,GO:0044424,GO:0044429,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0044763,GO:0046872,GO:0046914,GO:0046916,GO:0048878,GO:0050801,GO:0050896,GO:0051716,GO:0055065,GO:0055070,GO:0055076,GO:0055080,GO:0055082,GO:0055114,GO:0065007,GO:0065008,GO:0070887,GO:0071241,GO:0071248,GO:0072593 +TR3854|c0_g1_i1 GO:0003674,GO:0003824,GO:0003865,GO:0005575,GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229,GO:0016491,GO:0016627,GO:0031090,GO:0033765,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0071704,GO:0098588,GO:0098589,GO:1901360 +TR131|c0_g1_i1 GO:0031090,GO:0033765 +TR5075|c0_g1_i1 GO:0031090,GO:0033765 +TR2182|c3_g2_i6 GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175,GO:0004190,GO:0004518,GO:0004519,GO:0005488,GO:0006139 +TR3788|c0_g1_i1 GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229 +TR4859|c0_g1_i1 GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175,GO:0004190,GO:0004518,GO:0004519,GO:0005488,GO:0006139 +TR2487|c0_g1_i1 GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169 +TR2122|c0_g2_i2 GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872 +TR4277|c0_g1_i1 GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872 +TR3091|c0_g1_i1 GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169 +TR2130|c1_g3_i1 GO:0003674,GO:0003824,GO:0003865,GO:0005575,GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229,GO:0016491,GO:0016627,GO:0031090,GO:0033765,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0071704,GO:0098588,GO:0098589,GO:1901360 +TR3807|c0_g1_i1 GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005634,GO:0005743,GO:0005829,GO:0006801,GO:0006873,GO:0006875,GO:0006878,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0010035,GO:0010038,GO:0016020,GO:0016530,GO:0016531,GO:0016532,GO:0019725,GO:0019866,GO:0030003,GO:0030234,GO:0031090,GO:0031966,GO:0042221,GO:0042592,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044237,GO:0044422,GO:0044424,GO:0044429,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0044763,GO:0046872,GO:0046914,GO:0046916,GO:0048878,GO:0050801,GO:0050896,GO:0051716,GO:0055065,GO:0055070,GO:0055076,GO:0055080,GO:0055082,GO:0055114,GO:0065007,GO:0065008,GO:0070887,GO:0071241,GO:0071248,GO:0072593 +TR1894|c2_g1_i1 GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872 +TR5212|c0_g1_i1 GO:0003865,GO:0005575,GO:0005783 +TR939|c0_g1_i1 GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175,GO:0004190,GO:0004518,GO:0004519,GO:0005488,GO:0006139 +TR1891|c0_g1_i1 GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175 +TR2672|c0_g1_i1 GO:0003865,GO:0005575,GO:0005783 +TR2844|c0_g1_i1 GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234 +TR1837|c2_g1_i1 GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005737,GO:0006801,GO:0006810,GO:0006811,GO:0006812,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169,GO:0044237,GO:0044424,GO:0044464,GO:0044699,GO:0044710,GO:0044765,GO:0046872,GO:0046914,GO:0051234,GO:0055114,GO:0072593 +TR1678|c0_g1_i1 GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175 +TR3249|c0_g1_i1 GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175 +TR1479|c0_g1_i1 GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005737,GO:0006801,GO:0006810,GO:0006811,GO:0006812,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169,GO:0044237,GO:0044424,GO:0044464,GO:0044699,GO:0044710,GO:0044765,GO:0046872,GO:0046914,GO:0051234,GO:0055114,GO:0072593
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered/Trinity_filtered_exp.fasta Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,34 @@ +>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA +CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG +CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC +AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT +ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG +GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG +AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG +TATATGGTACAGATGTAAAG +>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT +TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT +ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA +TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC +>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT +TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA +TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT +TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT +AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT +ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA +AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC +CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG +GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT +G +>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA +GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC +AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC +CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC +ATACATGATTCTATTCAACCAA +>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG +CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT +ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA +TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered/Trinity_filtered_hi_iso.fasta Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,45 @@ +>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG +CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC +AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT +ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG +GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG +AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG +TATATGGTACAGATGTAAAG +>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT +TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT +ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA +TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC +>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA +ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC +AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG +AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA +AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA +>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT +TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA +TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT +TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT +AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT +ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA +AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC +CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG +GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT +G +>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA +GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC +TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG +TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC +>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC +AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC +CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC +ATACATGATTCTATTCAACCAA +>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG +CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT +ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA +TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered/Trinity_filtered_pct_iso.fasta Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,45 @@ +>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG +CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC +AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT +ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG +GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG +AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG +TATATGGTACAGATGTAAAG +>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT +TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT +ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA +TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC +>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA +ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC +AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG +AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA +AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA +>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT +TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA +TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT +TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT +AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT +ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA +AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC +CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG +GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT +G +>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA +GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC +TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG +TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC +>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC +AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC +CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC +ATACATGATTCTATTCAACCAA +>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG +CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT +ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA +TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered/counts.matrix Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,8 @@ + wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TRINITY_DN1_c0_g1_i1 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00 +TRINITY_DN0_c0_g1_i1 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00 +TRINITY_DN2_c0_g1_i1 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 +TRINITY_DN2_c1_g1_i1 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00 +TRINITY_DN2_c2_g1_i1 11.00 4.00 4.00 8.00 5.00 7.00 3.00 4.00 8.00 +TRINITY_DN2_c3_g1_i1 368.00 422.00 425.00 172.00 216.00 210.00 234.00 254.00 212.00 +TRINITY_DN3_c0_g1_i1 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/norm/Trinity.fasta Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,46 @@ +>TRINITY_DN1_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT +TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT +ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA +TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC +>TRINITY_DN0_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] +CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG +CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC +AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT +ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG +GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG +AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG +TATATGGTACAGATGTAAAG +>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] +TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA +ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC +AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG +AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA +AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA +>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT +TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA +TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT +TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT +AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT +ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA +AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC +CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG +GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT +G +>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] +ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA +GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC +TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG +TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC +>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] +GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC +AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC +CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC +ATACATGATTCTATTCAACCAA +>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG +CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT +ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA +TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/norm/Trinity_paired_unmerged_1.fasta Thu Jun 14 03:12:34 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 03:12:34 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw/Trinity.fasta Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,45 @@ +>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] +CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG +CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC +AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT +ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG +GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG +AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG +TATATGGTACAGATGTAAAG +>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT +TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT +ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA +TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC +>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] +TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA +ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC +AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG +AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA +AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA +>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT +TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA +TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT +TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT +AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT +ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA +AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC +CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG +GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT +G +>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] +ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA +GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC +TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG +TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC +>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] +GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC +AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC +CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC +ATACATGATTCTATTCAACCAA +>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG +CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT +ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA +TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw/Trinity_single_unmerged_1.fasta Thu Jun 14 03:12:34 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 03:12:34 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/raw/map.tsv Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,7 @@ +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.left.fq Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,400 @@ +@61DFRAAXX100204:1:100:10494:3070/1 +ACTGCATCCTGGAAAGAATCAATGGTGGCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTTT ++ +ACCCCCCCCCCCCCCCCCCCCCCCCCCCCCBC?CCCCCCCCC@@CACCCCCACCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:100:10497:13422/1 +GTAATTTCCGTACCTGCCACAGTGTGGGCTCACCCTGCTTAGAGGACAGGGAAGGACCCTAAAGGTAGGCTGATGC ++ +CCCCCCCCCCCCCCCCCCCCCCDCDCCCCCCCCCCCCCCCCCCCDDCCDDCDCBDCCDDDDBADDADDB@DBBBA@ +@61DFRAAXX100204:1:100:10546:4478/1 +CTGGGCTGCAGCTAAGTTCTCTGCATCCTCCTTCTTGCTTGTGGCTGGGAAGAAGACAATGTTGTCGATGGTCTGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC7CB@CA:>AB?C=C@@@@?A@?5:88: +@61DFRAAXX100204:1:100:10609:6818/1 +CACGTTTTCTAAGCAGTTTGTACCAGATCGTGCTAACTGCTCATTGTCTTGTTGTACACACCAGTAAAGCTGGGCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:100:10648:5988/1 +TGCTCATTGTCTTGTTGTACACACCAGTAAAGCTGGGCAAAAATATCATCCAAAAGTACATCGCTGAGAACTCCTA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCDCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:100:11486:13583/1 +CCCACCTGAAAACATTTTCTACATCCACTGTTATATGGAATGCTTGATAAGCTTTTCATTCTAACCATCAGAGCAC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBC +@61DFRAAXX100204:1:100:1176:14271/1 +TCTGAATAAGTCCTGCCACCAATGTTTTTCATAAGTGTGGCCATATGTTTTCATTATTTCAAACATTACTGTTAAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCDCDCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCDBBABDB +@61DFRAAXX100204:1:100:12152:16425/1 +CTCCGTTTTTTGAGAGTGCAACACATAGATACTGCTTGATAGCATTAATAAACATCTCATTTGTCCTGAAAACAGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:100:14680:13081/1 +GCCTGAGTGTGCAAAAATCTTCAGAGTAAGAATACCATAGTTGCTAAATATCTTTTACCATGAGCAATAATTTTTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC;CCCCCC +@61DFRAAXX100204:1:100:16086:14019/1 +TCTGGTGCAGCTAGATGGAATACTGAGAAAATGTTCTTCCATCCTGAACGAATATTTGCAGCCTGAGAATTAACCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCBCCDDCDCC +@61DFRAAXX100204:1:100:17458:1622/1 +GTGAAAGGTCATCTATTTTAATGGCTTGTCTTTAAAAACCCTAAGAGAGGGAGGATGTCACAGGGAGGGCTTGTCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCC5A############################################### +@61DFRAAXX100204:1:100:17716:21197/1 +CCAGGCTTCCCGGTGACTTTCGGATGTTAGAGTGAGGAAGTAGCTCAGCGCTTCCCTGCAGACGTTTAAAAGCCTC ++ +CCCCCCCCCCCCCBCCCCCCCCC@CCCCCC@BBCCCCCCCBDB>CCCCAC@BCBBCDDBD@?BCBA@6BBB>;A;: +@61DFRAAXX100204:1:100:19734:13092/1 +ATCATCTTGGAGACTTTTATCCACATCATGTGTTTGGGGCTCAAGATCCCCTTCATGCTCTTGGTTTATATGATCA ++ +;CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCDC +@61DFRAAXX100204:1:100:2082:1789/1 +ACGGGTGTGGTGCCAAGCATCCCTTGTTCTTGGAGGTATTGTATTCCTCTCTTTGGTTTCTTATTAAATAAATCAA ++ +CCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCADCCCDBCCCCCCCCCCDABBCCDCC@CBBBDDDD;@B?= +@61DFRAAXX100204:1:100:2172:8797/1 +GCCAAAACATAAGCAGTATCTGCACTAGCAAAAAGGGTTTGTCCTTGGTTGCACTCTAGGGATCTTGCAGCAAATT ++ +############################################################################ +@61DFRAAXX100204:1:100:2238:12815/1 +ACCATAGTTGCTAAATATCTTTTACCATGAGCAATAATTTTTTTCTCCCTTCCCCCACCCCCAATTATAAACATTT ++ +############################################################################ +@61DFRAAXX100204:1:100:2327:5980/1 +CTCCTAAATAATTTCCATCAGTGTGGGCCACCGTGATGAGTGTTTTTATTGTGTCGATATTCTTCTGTTTCATTTC ++ +CCCCCCCCCCCCCCCCCCCCCCCCC0BBBACCCBCCCCCC=CCCCCB@B@=DC@CCDDBCC-CC@CABBBB<CCCA +@61DFRAAXX100204:1:100:3665:17139/1 +ATACTTCTTTGGGTAATTTCCGTACCTGCCACAGTGTGGGCTCACCCTGCTTAGAGGACAGGGAAGGACCCTAAAG ++ +CCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCDCBCCCCCCCCCCCCCCCCCCCCCCCCBCBCDCCCBDBA>DC +@61DFRAAXX100204:1:100:6480:5393/1 +TGGAGACTTTTATCCACATCATGTGTTTGGGGCTCAAGATCCCCTTCATGCTCTTGGTTTATATGATCAACAGTCT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCBCCCCBDCBDDADBDC +@61DFRAAXX100204:1:100:8693:14085/1 +AGCTATTTCGTTATAAATGGCTGATAGATACTCTTCAGGGAGATCTTTACTGTCATTGATACCACGATTCATTTTA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:100:9306:14527/1 +GTAGAATGATGCGTGAGCTTTAAACCTGCTGTCACTGATCTTCAGAACTTTAGTGAGGAACAGTAACAGTAAGTTA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCBACDCCBCDCBCC +@61DFRAAXX100204:1:100:9656:2687/1 +CTTCTAGGCAAAGAGAGGCTACTTCAGTATCATCACAGTCTTGGAGACCCACACTGAATGCAGCCAGAAAAGGTGT ++ +BBBBBBBBBBBBBBBBBBBBB>>B>;=;=7>>?>>B>>;>BB>B################################ +@61DFRAAXX100204:1:101:11219:19264/1 +TTTGCTAACTTCTTCACTCACAGTAGAAACAGAAACCAGTGGTGCTTGCTGTCTGTTATCTGAAGATCTNGGTTGA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCABCCCCCCCCCCCCCC@CBCC;DB<>>A&>99>;@ +@61DFRAAXX100204:1:101:11349:8542/1 +GGGTAATTTCCGTACCTGCCACAGTGTGGGCTCACCCTGCTTAGAGGACAGGGAAGGACCCTAAAGGTANGCTGAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCAA;A'??@=@> +@61DFRAAXX100204:1:101:11674:10443/1 +CACCCACACCCTGTCTTCAGGTGCCACGCTCATGTCATCACTTGTGTACTCCTTGAAAGCCTGCGGTCTNTCAGAC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCACCCCCCCCCCACC&AAA?AC +@61DFRAAXX100204:1:101:1179:19106/1 +TTGGTTGAATAGAATCATGTATGTCTACAGATTTTTGTGATATTGCATCCAACGGCTTTTCACTCACAGNTGATGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@BCCCCCCCCCCCCCCCCCACCCCADCCBCA@'AA=@?? +@61DFRAAXX100204:1:101:12110:12654/1 +CTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATCCGGAAGAGAATGCGCAGCCCACACGCCAGGCNGCTTGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCBCCDCCBCCDCCDCBCDAD@ABBDDDAD@BABB.625'?A=:@0 +@61DFRAAXX100204:1:101:13165:4417/1 +CTGGATTATCAGTGCCAGACATCTGTGTACTGTAGCTGCCAATTCCTGATGATGATGTGGATTCTAAGGNGTTTAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCA?&75:;8C +@61DFRAAXX100204:1:101:13420:13159/1 +GGTGGATCCCCTCCTGTTGTCATCTTGACAGGCATCAGCCACAACAGATTCAGGGCACAGCAAGCCCTCNAAATGA ++ +CCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACAC&89848C +@61DFRAAXX100204:1:101:14810:10441/1 +CAGGAAAGAATCAATGGTGGCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTCTGNAATGCA ++ +CCCCCCCCCCCCCCCCCDCCCCCCCCCCBCBCCCBBCCCCCCCBCCCDCCCCCCCDCCDCCCDCC:A?A'AAAAAC +@61DFRAAXX100204:1:101:15025:8342/1 +GTGGGTAGGAAGCCTCTGCTGCAGGATCCTTTCACAGAGCAGAGCAATGTAAACACCAACAGAAAAACANCGGCTC ++ +CCCCCDCCCCC@CCCCCCCCCCCCCCCCCCCCCCCCCDCCCCBDBCCBCDCCCDCCDCBDACBBD=999%8====B +@61DFRAAXX100204:1:101:15551:15592/1 +CTCCCAAAACCATGCCAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATNTACATC ++ +CCCCCCCCCCCCCCCCCCCDCCCCCCCCCBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCA=7A'AAB?AC +@61DFRAAXX100204:1:101:16061:6897/1 +ATGGAATGCTTGATAAGCTTTTCATTCTAACCATCAGAGCACAGTTCACAGTATGAATACATTTCCAGTNAATCTA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCDCCCCCCCDCCCCDC=C@'ABAAAC +@61DFRAAXX100204:1:101:16516:11581/1 +GGCCCTAAAGGTAGGCTGATGCTGTGGGAACAGCCTTTCTGCTCAATATGAGCCCAACACGCGACAGAGNCCACTG ++ +74/8588857;-84;<<<<<-88;8488+8A<286A9AA##################################### +@61DFRAAXX100204:1:101:17825:1193/1 +ACGCTCATGTCATCACTTGTGTACTCCTTGAAAGCCTGCGGTCTATCAGACACATATTTTGCACAATGGNGAATAA ++ +BCCCCCCCCCCCCCCCDCCCCCCCCCCCC@CBCCCCCCC@CCCCCBCDCCCCCCCCCCCCCCCCCAABA&A>>??A +@61DFRAAXX100204:1:101:2920:3823/1 +TCCATCAGAGCACAGTTCACAGTATGAATACATTTCCAGTAAATCTAACCTCCCAAAACCATGCCAGGTNTGTTAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB'CCBC@C +@61DFRAAXX100204:1:101:4549:18278/1 +AGGTGGATCCCCTCCTGTTGTCATCTTGACAGGCATCAGCCACAACAGATTCAGGGCACAGCAAGCCCTNAAAATG ++ +AB?BA:?B<?>:>:7;=BB=??>A>>>:+>//000BBBB@B@BBBBABBBB>B@?ABBBBBB>@############ +@61DFRAAXX100204:1:101:5059:19347/1 +TTTGGACTTGCCTTTGAAGCCTGCTTTCCACAGAGCAGTCCTCTGTTCATTGTTGGAATTAAATGCTTTNGCAAAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCC&89:79C +@61DFRAAXX100204:1:101:5741:4886/1 +CCCACCCCCAATTATAAACATTTTATCCTTCAAAATACAGCTCTCCTGAGTTGTACTTCTCGCAGAAGCNCAGTCT ++ +CCCCCCBBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'B?BAAC +@61DFRAAXX100204:1:101:6207:10801/1 +GCCAAAACATAAGCAGTATCTGCACTAGCAAAAAGGGTTTGTCCTTGGTTGCACTCTAGGTATCTTGCANCAAATT ++ +DCCCCCCCDBCCCCCCCCCCCCCCCCCCCCCAC@CAA9AACCCCCCCC@CCCCCCCCCCB@CCCC########### +@61DFRAAXX100204:1:101:6228:11229/1 +CAGTGATTCAAGTTTCAGTCTGTGAAAGGTCATCTATTTTAATGGCTTTTCTTTAAAAGCCCTAAGAGANTGAGTA ++ +CBCCCCCCCCCCCCC@CCBBCC@CC@<BB@C@CC@CC?CBC?C<CCC?CCC?>>:<5?/:>A?:A########### +@61DFRAAXX100204:1:101:7284:17741/1 +CAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATCTACATCAAGCCCCGNCACCCA ++ +CCCCCCCCCCCCCCBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCC@'CCCCCC +@61DFRAAXX100204:1:101:7317:19738/1 +ATGAGAATCAATATTGTACAGAAAGTTGTACAGAATTTTTTTACATAGAAAACTTTACATCTGTACCATNTACATA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCACC'AAAAA@ +@61DFRAAXX100204:1:101:7386:20759/1 +CCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTCTGAAATGCAAGTTCTACTATGNTTTCAT ++ +CCCCCCCCCCCCCCCBBCCCCCCCCCCCBCCCCCCCDCCCCCCDCCBCCCCCCDCCBBCBCCCCCCBBC)ACBA@D +@61DFRAAXX100204:1:101:7661:3279/1 +TTGGGGCTCAAGATCCCCTTCATGCTCTTGGTTTATATGATCAACAGTCTGAGGTGGCAAATATCTAAGNTGAGGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCC'@????= +@61DFRAAXX100204:1:101:7989:14539/1 +CGTGCTCCAAGTGTGTTGCACTTGTAAAAGGTGCCTGAACATGGCTCACAGCTTCCATGAGTGCTTTAGNCGTCTT ++ +CCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCBDCCCCCCCCCABCCCCCBCCCCCCBCC=CBCCCCCCC'AA<A@C +@61DFRAAXX100204:1:101:8630:9416/1 +GAGGGAGACAGGCGAGTAGGTGGCGGTGGGGGCGAGGAGGCGTGGATGCTAGCCGCCGTCTCCGTTAGCNTCCGTC ++ +############################################################################ +@61DFRAAXX100204:1:101:9622:17436/1 +GCCAAAACATAAGCAGTATCTGCACTAGCAAAAAGGGTTTGTCCTTGGTTGCACTCTAGGTATCTTGCANCAAATT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCBBCCCBBBB'AAA=AC +@61DFRAAXX100204:1:102:10071:12692/1 +TGCGTGAGCTTTAAATTTAAAAGCCTCTGCTGGANTTCTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATCC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'CCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDBCCDCCDDAC +@61DFRAAXX100204:1:102:10556:11503/1 +TCCTGGGATTCCATTTGCTTGGATGTTTTCACTGNCACTACCATCTTCTACAGTTCCAGTGTTGCCTTCTGTACTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'BBBBBCCCCCCCCCCCCCCCCCBCBCDCDCCCDBDBCAABB +@61DFRAAXX100204:1:102:10558:14342/1 +ATGTTTTCTACCTTGGTGGATCCCCTCCTGTTGTNATCTTGACAGGCATCAGCCACAACAGATTCAGGGCACAGCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCC'CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBC +@61DFRAAXX100204:1:102:12109:19420/1 +TCTGTTATCTGAAGATCTTGGTTGAATAGAATCANGTATGTCTACAGATTTTTGTGATATTGCATCTTACCAACGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'>????DCCCCCCCCCCCCC@BACCCCCCBCDCCCDCDBDDB +@61DFRAAXX100204:1:102:12757:13134/1 +GGGATGTATTGAACCACTGCTCTCAGGACAGGAANAAACAATGCACAAGCAATTTTCTTCCTAAATAACAATTCAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC)BBBBBCCCCCCCCCCCCCCCCCC@BCCCCCCCCCCACCCCC +@61DFRAAXX100204:1:102:13549:15464/1 +GTCCATGTACATCCGGAAGAGAATGCGCAGCCCANACGCCAGGCTGCTTGTCTCCTGTTTTAGAAGATTGGGCTTG ++ +CCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCC'CCCCCCCCCCC?CCCDCCBCCCBDCDBDDBBCADA<AC@BB +@61DFRAAXX100204:1:102:13777:6235/1 +CGCAGGACTCACAAGGGTAAAGCAAATTAAGAACNCGTCTGTCTGCGGGTAGGAGAGGGGACGCAATCTGTCATAC ++ +############################################################################ +@61DFRAAXX100204:1:102:14960:18241/1 +GCCACGAATTTCCTAAATAATTTCCATCAGTGTGNGCCACCGTGATGAGTGTTTTTATTGTGTCGATATTCTTCTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC&CCCCCCCCCCCCCCDCCCCCB@BB@DCCCCDCBCCCCCCCC +@61DFRAAXX100204:1:102:15063:6971/1 +CAGAAAAGGTGTCCAAGCCAACTTAAACATCGGCNTCACGTGCTCCAAGTGTGTTGCACTTGTAAAAGGTGCCTGA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'8;9;9CCCCCCC@CBCCCCCCCCCCCCCCCCDCAACBBBBC +@61DFRAAXX100204:1:102:16420:15231/1 +GTTGTACTTCTCGCAGAAGCTCAGTCTTTACATCNATACTTCTTTGGGTAATTTCCGTACCTGCCACAGTGTGGGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCC'CCCBCCCCACCCCCCDCCCDCDDDCAB@BDBBDDCBCACCB +@61DFRAAXX100204:1:102:16908:12433/1 +CACTGATGAAATAATTCAAAAACTTTATTGACCTNTAACCTGATTAGATATGCCAGATGAGAATCAATATTGTACA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCC +@61DFRAAXX100204:1:102:17677:10400/1 +CGCACATCTTATCCCTTCTAGGCAAAGAGAGGCTNCTTCAGTATCATCACAGTCTTGGAGACCCACACTGAATGCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC',00.-;7;<4?@>:A########################## +@61DFRAAXX100204:1:102:17711:7491/1 +ACTCTGGACAATATCAAGTGGCTTTTCTTCATAGNCTCCATCATACAAGATATCATTTTTAGATAATGTTTCAGCT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCC'CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCDCCCCBCA +@61DFRAAXX100204:1:102:17798:2084/1 +CCTTGTTCTTGGAGGTTTTGTATTCCTCTCTTTGNTTTCTTATTAAATAAATCAATCCCTTGTTCTATTATTTCTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBB'BBBBBCCCCCCCCCCBBCCACCCCCCCCCCCCCCDCCCCCC +@61DFRAAXX100204:1:102:18807:10059/1 +CTGCACTGGAAATATCAGATCCGTTTTCAGGCTCNGTATCATCTTGGAGACTTTTATCCACATCATGTGTTTGGGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC&CBCCCCCCCCCC@CDCCCCCCCDCDCDC@ACDBADDBB;BA +@61DFRAAXX100204:1:102:19518:11565/1 +CCTGGGAAGAAGACAATGTTGTCGATGGTCTGGANGAGTTCCAGCTGCACAACACATTTAATCAACAGGGCAGCAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCC'BAB>BCCCBCCCCCCCDDACABCCBACCACDAD@DDBD<>C +@61DFRAAXX100204:1:102:2639:2051/1 +CTGCCTCAGAGAGTCTACTGCAAATATGGCTACANCTTCATTAGGATTACAACCAACCTTATTAAAATGATCTCCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCAA3A########################################## +@61DFRAAXX100204:1:102:3101:2926/1 +CTTCCCAGGCACTGACTCTGCTCTCGTCCATGTANATCCGGAAGAGAATGCGCAGCCCACACGCCAGGCTGCTTGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'BBBBBCCBCCCCCCCCCCCCCCCCCCC<CCCDDCAAB@B<B +@61DFRAAXX100204:1:102:5977:14503/1 +GGGGGTTCGGCCTCGCCAGAGGTGGGACGCCAAGNCAGAAGCGCGTGAGGAATTGTGGTTTTGAAGATATCCAGGG ++ +CCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCCC'CCCCCCCCCCDCACCBCBCC?CCBCCCCAACDCCCBCDCCA +@61DFRAAXX100204:1:102:6251:21399/1 +CCCAGCTATTTCGTTATAAATGGCTGATAGATACNCTTCAGGGAGATCTTTACTGTCATTGATACCACGATTCATT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'BBBBACCCCCCCCCCC@CCCDCCCCCDCDCCBCCBCDD@CC +@61DFRAAXX100204:1:102:7093:4246/1 +CGGGTCTTGTCAGCAGGGATGTTTTCTACCTTGGNGGATCCCCTCCTGTTGTCATCTTGACAGGCATCAGCCACAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC(CCCCCCCCCCB@CDCCDCCCCCCCDDDCBDDBDDBDCDABB +@61DFRAAXX100204:1:102:7907:21314/1 +AGACACATATTTTGCACAATGGCGAATAAGTCGGNTTGCTTCCATACTTGTGTCTGGGAAAGCTGCATTACATGCG ++ +>BBB>BB>BBB<B?>?>??<99:<9:A<??0000%*000089:;<74;?8BABBBBA>B################# +@61DFRAAXX100204:1:102:8037:6949/1 +TCTAGGTATCTTGCAGCAAATTTTTCCATTAATCNATCAATTTTCTGAGCTTCTCCTGGAAGCCGGAATCCTTCCA ++ +CCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCC(BBBBBCCCCCCCCCCCCCCCCCCCBCCCCCCDDDCCCCCCC +@61DFRAAXX100204:1:102:8724:1888/1 +CGGGTGTGGTGCCAAGCATCCCTTGTTCTTGGAGNTATTGTATTCCTCTCTTTGGTTTCTTATTAAATAAATCAAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBB@B&28;88DCCCCCCCCCCCCCCDCCCCCBCCDC@BCA>@BD@B +@61DFRAAXX100204:1:102:8903:16361/1 +CCTATAAGTTGTGCCAGCTCTAACTGACTGATGCNCTTCAGGATCTCATGCCACGAATTTCCTAAATAATTTCCAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC(CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:102:9691:18717/1 +ATAAGTTGTGCCAGCTCTAACTGACTGATGCACTNCAGGATCTCATGCCACGAATTTCCTAAATAATTTCCATCAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'BABBACCCCCCC;CCCCCBCCCCCCCCCCCCCCCCDCCCAC +@61DFRAAXX100204:1:103:10201:1449/1 +CTGAACACTAGAAAGGCATCCTTTTGTAAAATGTGGGAAAACTTAGCACCAGGTGAAGGTCCTGAAGAATTTCCAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCCCDCCCCCCCC?CCBCCCCCACC;CCCCCCC +@61DFRAAXX100204:1:103:11572:6697/1 +CAAAATTGAAACTAAACATTCTAACCCCTTTTTTCGCAGGCTCAATTCCTGAACATTACTCATACCGAGTTCTTGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC8CDCCCCDD +@61DFRAAXX100204:1:103:12517:20251/1 +GCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTCTGAAATGCAAGTTCTACTATGCTTTCAT ++ +CCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:13105:12342/1 +CTGGACTTCTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATCCGGAAGAGAATGCGCAGCCCACACGCCAGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCBCCCB@CCCCCB?BCCCCCCB@C@B; +@61DFRAAXX100204:1:103:13548:1359/1 +GGTGACTTTCGGATGTTAGAGTGAGGAAGAAGCTCAGCGCTTCCCTGCAGACGTTTAAAAGCCTCTGCTGGACTTC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCC+??AA?CCCCCCCCCCDCCDCBDCBCC@BBDDBDDDDBBABBACAAB +@61DFRAAXX100204:1:103:13762:1440/1 +CTCCCTTCCCCCACCCCCAATTATAAACATTTTATCCTCCAAAATACAGCTCTCCTGAGTTGTACTTCTCGCTGAA ++ +CCCCCCCCCCCCCBBBBBBCCCCCCCCCC?CCCCCCCCCCCCACCCCCCCCCCCCCCCCDCCDCCCCCCCACCBB@ +@61DFRAAXX100204:1:103:13776:4298/1 +TGATATTTGAAATACTATTCCAATTCGCAGGAAAAATCTTCTAAGAACAGCACGCAGTTCCGGAATCAAGTCAAAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDC@BCC +@61DFRAAXX100204:1:103:13798:6365/1 +GGTCACAGTCATAATTTACATAAATGTCCACCACACTCTGAGCATCTGCACAGATCCTTGTCAGTGTCTGAATAAC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCC +@61DFRAAXX100204:1:103:14748:1375/1 +CCAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATCTACATCAAGCCCCGCCACCC ++ +CCCCCCCCCCCCCCCBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@BCCCCCCCCCACCCDBD@@DDB +@61DFRAAXX100204:1:103:16156:9928/1 +CATGAGCAATAATTTTTTTCTCCCTTCCCCCACCCCCAATTATAAACATTTTATCCTTCAAAATACAGCTCTCCTG ++ +CCCCCCCCCCCCCCCCCCBBBBCCCCCCCCCC@B@BB@CCCCCCCCCACCCCCCCCCCCCAACCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:16292:7311/1 +CTGGTTCTTACATCTAATTTGCATCTATTGATGATACAAGACAACTCAAAGAGGATCGGGAACCACCCTCTCACCC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDBCDCDCCCCCCCCCCBDC +@61DFRAAXX100204:1:103:1757:15756/1 +GGCAAAAATATCATCCAAAAGTACATCGCTGAGAACTTCTAAATACTGGGTGAATACATCACATATTGCATAAAGG ++ +CCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:19512:1223/1 +CTGTTAAGCCCCTGGTTCTTACATCTAATTTGCATCTATTGATGATACAAGACAACTCAAAGAGGATCGGGAACCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCDCCDADBB@C@BB@ +@61DFRAAXX100204:1:103:2005:9846/1 +TGCTTCCCTGCAGACGTTTAAAAGCCTCTGCTGGACTTCTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCBCCCCABDBBCBBDDDC +@61DFRAAXX100204:1:103:2755:14644/1 +CTTACATCTAATTTGCATCTATTGATGATACAAGACAACTCAAAGAGGATCGGGAACCACCCTCTCACCCACACCC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC=C +@61DFRAAXX100204:1:103:3597:13520/1 +GTTGTTGTGATGTTAAAAAGCGGTACATTCCTTGGTCTTGAGTATCAACTCGAACATCGAAGTCTACTACATCTCT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCDCCCCCCCCCCCCCCCCCDCBCCCCDADDCDCDC +@61DFRAAXX100204:1:103:4062:11566/1 +GATGATACAAGACAACTCAAAGAGGATCGGGAACCACCCTCTCACCCACACCCTGTCTTCAGGTGCCACGCTCATG ++ +CCCCCCCCCCCCCBCCCCCCCCCCCCBCCCCC@CACCBCCCCCCCCCACCBCC=@BCBAC3;;-6AC@C@C?@:AB +@61DFRAAXX100204:1:103:5147:16732/1 +CATGGTTACAAGTTGTTGTCATCCATTCAGCTTTCTCTGTCTGCTGTTCTGGCAATTTCATGTTGTCAAAGATTCT ++ +CCCCCCCCCC;????CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:6646:12936/1 +GTGCAACACATAGATACTGCTTGATAGCATTAATAAACATCTCATTTGTCCTGAAAACAGGTCCTGCATTCTGCAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCDC +@61DFRAAXX100204:1:103:7220:15954/1 +GAGGAATTGTGGTTTTGAAGATATCCAGGGTGCAGTTACACGTTTTATCCCAGATTTCAAGAGTAAACTTTTCACC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCABCCCCCCCA +@61DFRAAXX100204:1:103:7253:3680/1 +CTTTACATCTGTACCATATACATATCCACCTGAAAACATTTTCTACATCCACTGTTATATGGAATGCTTGATAAGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:8055:11636/1 +TTCCTGATGATGATGTGGATTCTAAGGAGTTTAAACTTCCATATCTGTTTATAGTCTCTGGGTGTTTAACTTCACT ++ +CCCCCCCCCCCCCCCCCC<CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCBCDCCCABCCCDCC +@61DFRAAXX100204:1:103:8348:14452/1 +GTCAGAGCACAGTTCACAGTATGAATACATTTCCAGTAAATCTAACCTCCCAAAACCATGCCAGGTTTGTTATTTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDBCCDCCCDCCCBCB +@61DFRAAXX100204:1:104:12460:3347/1 +CTGATGCTGTGGGAACAGCCTTTCTGCTCAACATGAGCCCAACACGAGACAGAGGCCACTGGGTTACTAAAGGGAC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCC@CCDCDDCCCCBCCDCBB@BBAAB +@61DFRAAXX100204:1:104:12993:12947/1 +GGTGAATACATCACATATTGCATAAAGGACATGGTTACAAGTTGTTGTCATCCATTCAGCTTTCTCTGTCTGCTGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:104:13501:6860/1 +GTGATATTTGAAATACTATTCCAATTCGCAGGAAAAATCTTCTAAGAACAGCACGCAGTTCCGGAATCAAGTCAAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCBCCCCCCACCCDCBCC>A
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.right.fq Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,400 @@ +@61DFRAAXX100204:1:100:10494:3070/2 +CTCAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCATCTAGCTGC ++ +C<CCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCACCCCCACCC= +@61DFRAAXX100204:1:100:10497:13422/2 +GAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCACCC +@61DFRAAXX100204:1:100:10546:4478/2 +CTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@BCDCBCCCCCCCCCCCACCCCCCCCCBDC +@61DFRAAXX100204:1:100:10609:6818/2 +AGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGCCCTTTATGCAATATGTGATGTATTCACCCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?CBCC +@61DFRAAXX100204:1:100:10648:5988/2 +AGATGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCACCCBCCBACC +@61DFRAAXX100204:1:100:11486:13583/2 +CTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCBBBB@CCDCCCCDB@BDCCABCDDCBBCCCBC@ +@61DFRAAXX100204:1:100:1176:14271/2 +TGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCG ++ +CCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCDCCCCCCCCCC:BBBACCABC@CDDAB@DDCABDDABDBB +@61DFRAAXX100204:1:100:12152:16425/2 +CCTTTCTAGTGTTCAGGTCATTGTGTAAGCTGTCAATGAAACCACTGTCAGATGGACCACCAGATCCAAAGTCTCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCC= +@61DFRAAXX100204:1:100:14680:13081/2 +CACAGCATCAGCCTACCTTTAGGGTCCTTCCCTGTCCTCTAAGCAGGGTGAGCCCACACTGTGGCAGGGACGGGAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCDCCCCCCCCCBCCDCCB'299@'9@ +@61DFRAAXX100204:1:100:16086:14019/2 +AGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACGACCTTTTGAACATATAATGAAACGAAACAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCBCCCCCC +@61DFRAAXX100204:1:100:17458:1622/2 +AAAACATTTGGGTTGAACTTTTAGTCTTTGGGGGAGTGGTGGTCATTTTGAGGGCTTGCTGTGCCCTGAATCTGTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@CCCCCBCCCCCCCDCCCDDCBDCBB@BABA=BBDB@AB< +@61DFRAAXX100204:1:100:17716:21197/2 +GCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCAC?CCDBBCCBD@BCBBBB@B??BBA=@A?@ +@61DFRAAXX100204:1:100:19734:13092/2 +GGCTTTACTTACCGCAGTGACATCACAACACATAGAAATCCATGAAGGAACTGTGCTGCAAGCTGTGAGGACATGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCC?CC@CBCCCBCAACCC +@61DFRAAXX100204:1:100:2082:1789/2 +GGAGCAAGGATCAGTATGTGAACCCCAACTCTCAAACTACCCTTGGTCAGGAAAAACCCTCAGAGCAAGAGATACG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCBCBCCCBCDBBDACCDBCDCA@B## +@61DFRAAXX100204:1:100:2172:8797/2 +TATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAA ++ +############################################################################ +@61DFRAAXX100204:1:100:2238:12815/2 +CCCCTCCAGACCCTTTAGAAACCCAGAGGCCTCGGGCTCGCGTGTGGCTCATTTTCGCCAGAAAGGCGGTTCCCAC ++ +############################################################################ +@61DFRAAXX100204:1:100:2327:5980/2 +CAAGACTGTGATGATACTGAAGTAGCCTCTCTTTGCCTAGAAGGGATAAGATGTGCTATCAGGATTGCATGCATTT ++ +CCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCACCCC?BCCCCACBCCBCCCCCCCDDDAA@CCDBBC +@61DFRAAXX100204:1:100:3665:17139/2 +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?CCCCCC@CC@@CB@@@@DABBBCBBB +@61DFRAAXX100204:1:100:6480:5393/2 +TGCTACAATATCTATTTAGCCAGCAAAAATCTCATCAATCAGACAACAGCCAAAGCTACTCTTACTGAAATGCTGA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB +@61DFRAAXX100204:1:100:8693:14085/2 +TGCAACCAAGGACAAACCCTTTTTGCTAGTGCAGATACTGCTTATGTTTTGGCCTACTCAATTATCATGTTGACTA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:100:9306:14527/2 +GCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGCTACTTCCTCACTCTAACATCCG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCC +@61DFRAAXX100204:1:100:9656:2687/2 +TAGAAATGGAACAGATGGCCAAGACGGCTAAAGCACTCATGGAAGCTGTGAGCCATGTTCAGGCACCTTTTACAAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCD3DBBCCCDCBBCCDCBDC +@61DFRAAXX100204:1:101:11219:19264/2 +GTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@B@CBBCCCADDCCA@BC +@61DFRAAXX100204:1:101:11349:8542/2 +GTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?DDD@CDDDDDBCBBCDDDBDABB)BBBB +@61DFRAAXX100204:1:101:11674:10443/2 +CTCTGAGGCAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACG ++ +CCCCCCCCCCC@CCCCBC?CC@CBBCCC=C@CCCCAC:B@BBCC>@=@@@B>@BC@ACBB@>CBB=0;C@BBCC/? +@61DFRAAXX100204:1:101:1179:19106/2 +AAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCBCCBBCCCCACCCCACCCCCCCCCCCCCCCCBABDB>D@BDDD@ +@61DFRAAXX100204:1:101:12110:12654/2 +GCAAGCACCACTGGTTTCTGTTTCTACTGTGAGTGAAGAAGTTAGCAAAGTGAAATCCACAGCAAAATTCCCAGAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCBCDCCCCCBCCCCCDCCBCDCCBCAACCDCCAA>BBC=B<B?B +@61DFRAAXX100204:1:101:13165:4417/2 +GGACATTTATGTAAATTATGACTGTGACCTAAATGCAGCAAATATATTTGAAAGACTAGTAAATGACCTGTCGAAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCAC +@61DFRAAXX100204:1:101:13420:13159/2 +CCGGAAATCATCATCTTTCTGTGAAAATGTACAGAGATGCAGGTCTGTAATATAAAAATCTTAAACATATTGTTCC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCDCCCCCCCCC@@CCCCBCCCCCCDCDBC@ +@61DFRAAXX100204:1:101:14810:10441/2 +GGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCBCCCCCC +@61DFRAAXX100204:1:101:15025:8342/2 +GCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCDCCDCDCACCB +@61DFRAAXX100204:1:101:15551:15592/2 +GACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCCCCCCCCCDCC@ +@61DFRAAXX100204:1:101:16061:6897/2 +GGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCC +@61DFRAAXX100204:1:101:16516:11581/2 +GATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTA ++ +C@CCCCCC@CCCCBBCBBCCC=@8@CC:CCCBC?C@@CC@C@>@@CCC>C>@>A<A8@8=<??<<=:C5>BCCBCC +@61DFRAAXX100204:1:101:17825:1193/2 +AACGAAGCAGGTCTCCAACAATTCGAGATATGGTTGTACGGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCCCCCCCCCCCBCCCCCCACCCDC<ABBBA +@61DFRAAXX100204:1:101:2920:3823/2 +CAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCA ++ +CCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCBCCCCCCCCCCCDCCCCCCCACCCCCCC=C? +@61DFRAAXX100204:1:101:4549:18278/2 +GTCTGTAATATAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTA ++ +CCCCCCCCCACCCCC@@CCCBB?CCCCCCCCCCCCCCCCCCCCCCCCCCC@@@CC@=CC@@@C@@CCCCCCCCACC +@61DFRAAXX100204:1:101:5059:19347/2 +AAGAAGACAATGTTGTCGATGGTCTGGATGAGTTCCAGCTGCACAACACATTTAATCAACAGGGCAGCAAACAATT ++ +CCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCDCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCCBCDADCA?ACC +@61DFRAAXX100204:1:101:5741:4886/2 +GGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTT ++ +CCCCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCACCCCBCC:CCCCCDCDCDCBCBCBC@BCCC@?BBCBCCBD +@61DFRAAXX100204:1:101:6207:10801/2 +GGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT ++ +CCCCCACCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCBCCCCACCCCCCCCD@BCBB@BBCABC +@61DFRAAXX100204:1:101:6228:11229/2 +CTGTAATATAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTAAA ++ +CCBBCCCCCCCCC@@CCC>CCCBBC??>@BCCCCCBBCCCCC@CCCBC@@@CC@@CC@@@C@>CCCCCCCCCCC@C +@61DFRAAXX100204:1:101:7284:17741/2 +AAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTAAATACCCATAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBCCB@CCBBBCBBCCCCCCCCCBCCCCCCCCCCBA +@61DFRAAXX100204:1:101:7317:19738/2 +CATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCBCCCCCCAAC?BCCCCDCCCCCDC@ +@61DFRAAXX100204:1:101:7386:20759/2 +GATGTAGCCATATTTGCAGTAGACTCTCTGAGGCAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCD@CACBDDB@CABCCCB@BBABBAABB>>BAB>?AA>AB +@61DFRAAXX100204:1:101:7661:3279/2 +GCTGCAAGCTGTGAGGACATGCTACAATATCTATTTAGCCAGCAAAAATCTCATCAATCAGACAACAGCCAAAGCT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCD@CCC +@61DFRAAXX100204:1:101:7989:14539/2 +TGACTACAGACCTTCACAGTCCACAGGTTAAAAACAAAATGACAAAAGAACAGTACATTAAAATGAATCGTGGTAT ++ +CDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBBBCCCCCCCC?BBCCCCCCCCCC@CCCCCCC?BCCBC= +@61DFRAAXX100204:1:101:8630:9416/2 +GGCGCAGGCACCTCCACCGGCCCCGCCTTCTCTCCGCAAACGCTCCACGCACACAAAGGAGGCCCTTGAGCCTCAA ++ +############################################################################ +@61DFRAAXX100204:1:101:9622:17436/2 +ACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCACCBCCCBCCCCCCCC +@61DFRAAXX100204:1:102:10071:12692/2 +GCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACCGCTTTTTAACATCAC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCDCCCCCDCCCCDCCCCCBC +@61DFRAAXX100204:1:102:10556:11503/2 +CGGATCTGATATTTCCAGTGCAGAAAATGAACAGACAGAAGCTGATCAGGCAACTGCAGCTGAAACATTATCTAAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCDCCC +@61DFRAAXX100204:1:102:10558:14342/2 +AGAGATGCAGGTCTGTAATATAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBCCBBCCBBBCBBC +@61DFRAAXX100204:1:102:12109:19420/2 +AAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCBCCC@CCCCCCCC?CCBCCADCDCAB +@61DFRAAXX100204:1:102:12757:13134/2 +CAACGGAGCAGATTGCGTCTCACACAGAGGAACGAGAGGAAGTCTGTAACGCTCAGAGACTTGATGACAGTTCTTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCBCCCDCCCCCBCDCDCDDDDDBDCBBBDCBDBDD +@61DFRAAXX100204:1:102:13549:15464/2 +GCAAGAAGGAGGATGCAGAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCA ++ +CCCCCCCCCCCCCCCCCCBCDCCCCCCCCCBCCCCCCCCCCCCCBCCCACC@CCCCCCCBDCCC=CC?CC?CCACA +@61DFRAAXX100204:1:102:13777:6235/2 +GAAGGCCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACACGACCATGAGCCGC ++ +############################################################################ +@61DFRAAXX100204:1:102:14960:18241/2 +GCTGCATTCAGTGTGGGTCTCCAAGACTGTGATGATACTGAAGTAGCCTCTCTTTGCCTAGAAGGGATAAGATGTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCACCCCCCCCCDC +@61DFRAAXX100204:1:102:15063:6971/2 +GTATCTATCAGCCATTTATAACGAAATAGCTGGGAAAAAAATATCAATGAAAGAAACAAAAGAACTAACAATCCCT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBBCCCCCCCCCCCBBCC@BBCBBCCCCC?CCCAC +@61DFRAAXX100204:1:102:16420:15231/2 +CTACTACCCTCTCTTATGTGAAATTATGCAATTTGACTTGATTCCGGAACTGCGTGCTGTTCTTAGAAGATTTTTC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCC@CCCCCCCC>@CCCCCCCCCBC@DCBCCC +@61DFRAAXX100204:1:102:16908:12433/2 +TGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCDCCCCCBCCACCCCBCC +@61DFRAAXX100204:1:102:17677:10400/2 +CAATCCCTACAAAGTCAACTAAACAGAATGTAGCCAGTGAAAAGCAAAGACGACTTCTGTATAACTTAGAAATGGA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCBCCCCACDCC;@BBB@C +@61DFRAAXX100204:1:102:17711:7491/2 +TATAAACCAAGAGCATGAAGGGGATCTTGAGCCCCAAACACATGATGTGGATAAAAGTCTCCAAGATGATACAGAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCDCCCCCCCADC=DCCBCDA +@61DFRAAXX100204:1:102:17798:2084/2 +AGTGAAGTTAAACACCCAGAGACTATAAACAGATATGGAAGTTTAAACTCCTTAGAATCCACATCATCATCAGGAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCDC +@61DFRAAXX100204:1:102:18807:10059/2 +CTACAATATCTATTTAGCCAGCAAAAATCTCATCAATCAGACAACAGCCAAAGCTACTCTTACTCAAATGCTGAAC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCACC +@61DFRAAXX100204:1:102:19518:11565/2 +CTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCBCC@BCCCDBCCDABDDDDCDBCBDCBDDA +@61DFRAAXX100204:1:102:2639:2051/2 +CAGGAGTCTATTGGAGAAACCAGCTCTCAAAGTGTGGTAGTTGCTGTGGATAGAATATTCACCGGATCCACAAGGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCDCCACCDCCCCCACCBCB@<A88>>5?>@>@17>A1;5;:=; +@61DFRAAXX100204:1:102:3101:2926/2 +GAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACC ++ +CCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCACCCCCCCCCCCDBCC +@61DFRAAXX100204:1:102:5977:14503/2 +GAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCDCDCDCCCCCCDCDCCCCCDBCDCB +@61DFRAAXX100204:1:102:6251:21399/2 +GTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCDCCCCDCCCCDCACCBCBCCBDDCC@D<BCBDDBDAB +@61DFRAAXX100204:1:102:7093:4246/2 +GAAGATTTTTGCACACTCAGGCTATCTGAGACACCGGAAATCATCATCTTTCTGTGAAAATGTACAGAGATGCAGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCBCCBCB@ABBBADB@C= +@61DFRAAXX100204:1:102:7907:21314/2 +GACTCTCTGAGGCAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGACTTCT ++ +@@@9@####################################################################### +@61DFRAAXX100204:1:102:8037:6949/2 +CTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAA ++ +CCCCCCCCCCCDCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCDCCCCCCCCADCBCCABCAD@C@ +@61DFRAAXX100204:1:102:8724:1888/2 +TGAACTCCTTAGAATCCACATCATCATCAGGAATTGGCAGCTACAGTACACAGATGTCTGGCACTGATAATCCAGA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@=B?@99;>?BB==<@=@A?B=<<BBB>DB2(?=;@ +@61DFRAAXX100204:1:102:8903:16361/2 +GCATTTTCAGCATTCAGCTGGAAAGAGATGCATATGTCCAAGCACTAGCCAGATTTACCTTACTTACAGTGAGTTC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCBCBCC +@61DFRAAXX100204:1:102:9691:18717/2 +CTAGAAGGGATAAGATGTGCTATCAGGATTGCATGCATTTTCAGCATTCAGCTGGAAAGAGATGCATATGTCCAAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:10201:1449/2 +GAGACTATGAAGAAAAGCCACTTGATATTGTCCAGAGCATTGTAGAAGAAATGTTGAACATCATTGTTGGAGACAT ++ +CCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCBCCCCCCCDCBCCCCDCCCCCCCDCCCCDCA@BCBBB? +@61DFRAAXX100204:1:103:11572:6697/2 +AGCTCATTTGACCATAAGTGGATGGTTATTCAGACACTGACAAGGATCTGTGCAGATGCTCAGAGTGTGGTGGACA ++ +CCCCCCCCCCCCCCCCCCAC???AAACCCCCCCCCCCCCCCCCCCBCCCCCCCC@CABCCCCAACBC>CB<A?:BB +@61DFRAAXX100204:1:103:12517:20251/2 +CAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACGACCTTTTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCCCCDDCDCCCCCCCDCDDDBCD +@61DFRAAXX100204:1:103:13105:12342/2 +TCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCBCDD@BAAA +@61DFRAAXX100204:1:103:13548:1359/2 +GGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCBDCDCCCBDCCCBDDBCCDDCDCADDBDC@B +@61DFRAAXX100204:1:103:13762:1440/2 +GAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCBCCCCCCCCDCCCDDCBCCCCB@BCC> +@61DFRAAXX100204:1:103:13776:4298/2 +CCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCBCCCCCCCC +@61DFRAAXX100204:1:103:13798:6365/2 +GTTTATTAATGCTATCAAGCAGTATCTATGTGTTGCACTCTCAAAAAACGGAGTCTCATCTGTTCCAGAGGTTTTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCCCCCCDCCDDCDCCBDDC@ +@61DFRAAXX100204:1:103:14748:1375/2 +TAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTAAATACCCATA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@BCCB=CCBBBC@@CCCACCCACCCCBCCCDD>DC +@61DFRAAXX100204:1:103:16156:9928/2 +CTCATGTTGAGCAGAAAGGCTGTTCCCACAGCATCAGCCTACCTTTAGGGTCCTTCCCTGTCCTCTAAGCAGGGTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCDCCCDCCDCCA@ACBABB?B +@61DFRAAXX100204:1:103:16292:7311/2 +CACCATTGATTCTTTCCAGGATGCAGTGAAGTGTTTGTCTGAATTCACATGTAATGCAGCTTTCCCAGACACAAGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCC5CCCCDCCCCCBCCBCCCBDDDBDBBBBCD +@61DFRAAXX100204:1:103:1757:15756/2 +TGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:19512:1223/2 +TGTCACTCTTGTATTTGAAAAACACTTTCCGGCCACCATTGATTCTTTCCAGGATGCAGTGAAGTGTTTGTCTGAA ++ +CCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCC@CBA8=A=CCACCCBCCA# +@61DFRAAXX100204:1:103:2005:9846/2 +TTTAATTCCAACAATGAACAGAGGGCTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA ++ +CCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBDDBCDCCDBDCBCCDDDCDADBBDDC +@61DFRAAXX100204:1:103:2755:14644/2 +GCTGCATCAGACCAAGATGAAAGCATAGTAGAACTTGCATTTCAGACAACAGGGCACATTGTCACTCTTGTATTTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCACCCCC>CCC@CBACDCCDCC +@61DFRAAXX100204:1:103:3597:13520/2 +CACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCACACDDCCDDCCB@A?B@BB@ABBBBADABD<?>AA +@61DFRAAXX100204:1:103:4062:11566/2 +CAACAATTCGAGATATGGTTGTACGGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATG ++ +CCCCCCCBCCCCCCCCCCCCC?CCCC=CCCCCA=@A@CCACBCC?ABAABCCCCACC>BC<CCCACCCCB@C@B@? +@61DFRAAXX100204:1:103:5147:16732/2 +GGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCBCCCBCCCCCCCBCCBBCCBC +@61DFRAAXX100204:1:103:6646:12936/2 +CTCCAATGATACTCAGGAATCTGGAAATTCTTCAGGACCTTCACCTGGTGCTAAGTTTTCCCACATTTTACAAAAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCC@CDCCDCCCCCDCCCDBDBADDC +@61DFRAAXX100204:1:103:7220:15954/2 +GATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBCCCCCCCCCCCCCBCDC +@61DFRAAXX100204:1:103:7253:3680/2 +GTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTT ++ +CCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@BCCCCCCCBCDCCCBCCCCCCB=CDA +@61DFRAAXX100204:1:103:8055:11636/2 +AAATGACCTGTCGAAAATTGCACAAGGAAGGGGCAGCCAAGAACTTGGTATGAGTAATGTTCAGGAATTGAGCCTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCDCCCCDACCCCCCCCCACCCCC +@61DFRAAXX100204:1:103:8348:14452/2 +AACATTTGGGTTGAACTTTTAGTCTTTGGGGGAGTGGTGGTCATTTTGAGGGCTTGCTGTGCCCTGAATCTGTTGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@CCCCCDCCCCCCCCCCCCCACBCCDCCCCCAB@CBCCDCBB +@61DFRAAXX100204:1:104:12460:3347/2 +CACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTTACATTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCBCCC@@@BBCCCACBCCC@ACBC +@61DFRAAXX100204:1:104:12993:12947/2 +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTTGCCATTGTGCAAAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCC@CCACBCDDCBCC,BBC?BBBBB@BBBD +@61DFRAAXX100204:1:104:13501:6860/2 +CTGAGCTACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samples.tsv Thu Jun 14 03:12:34 2018 -0400 @@ -0,0 +1,4 @@ +ConditionA CondA_replicate1 +ConditionA CondA_replicate2 +ConditionB CondB_replicate1 +ConditionB CondB_replicate2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/supertranscripts/trinity_genes.fasta Thu Jun 14 03:12:34 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 03:12:34 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" +