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Changeset 0:d4128a4e49ca (2016-11-21)

Next changeset 1:c8efaf2e5ed5 (2016-12-13)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c

diff -r 000000000000 -r d4128a4e49ca README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,18 @@
+Trinity memory usage
+====================
+
+As described on the official Trinity website
+`FAQ <http://trinityrnaseq.sourceforge.net/trinity_faq.html#ques_comp_resources_required>`_,
+trinity requires a large amount of memory to perform the assembly: "roughly
+~1G of RAM per 1M reads to be assembled"
+
+By default, this tool is configured to limit the memory consumption to 30G.
+You might need to lower this limit if the machine(s) executing the jobs have less memory available.
+If you have a lot of reads to assemble and a machine with enough memory, you can increase it.
+In both cases, you can edit the TRINITY_MEM_OPTIONS in the file:
+
+<tool_dependency_dir>/environment_settings/TRINITY_MEM_OPTIONS/iuc/trinity/<hash_string>/env.sh
+
+to lower the maximum memory usage to 2G for example:
+
+TRINITY_MEM_OPTIONS='--max_memory 2G --bflyHeapSpaceMax 2G'

diff -r 000000000000 -r d4128a4e49ca analyze_diff_expr.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/analyze_diff_expr.xml Mon Nov 21 11:59:35 2016 -0500

[

b'@@ -0,0 +1,179 @@\n+<tool id="trinity_analyze_diff_expr" name="Extract and cluster differentially expressed transcripts" version="@WRAPPER_VERSION@.0">\n+ <description>from a Trinity assembly</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements">\n+ <requirement type="package" version="2.30.0">bioconductor-biobase</requirement>\n+ <requirement type="package" version="2.2.2">bioconductor-qvalue</requirement>\n+ <requirement type="package" version="1.22.0">bioconductor-goseq</requirement>\n+ <requirement type="package" version="3.3.0">bioconductor-go.db</requirement>\n+ </expand>\n+ <expand macro="stdio"/>\n+ <command><![CDATA[\n+ ## DE results input files must be in the working directory and have suffix .DE_results\n+ #import re\n+ #for $input in $DE_results\n+ ln -s "${input}" "${re.sub(\'[^\\w\\-_.]\', \'_\', input.element_identifier)}.DE_results"\n+ &&\n+ #end for\n+\n+ analyze_diff_expr.pl\n+ --matrix "${matrix}"\n+ --samples "${samples}"\n+ -P ${p}\n+ -C ${c}\n+\n+ #if str( $additional_params.max_DE_genes_per_comparison ):\n+ --max_DE_genes_per_comparison ${additional_params.max_DE_genes_per_comparison}\n+ #end if\n+\n+ $additional_params.order_columns_by_samples_file\n+\n+ #if $additional_params.max_genes_clust:\n+ --max_genes_clust ${additional_params.max_genes_clust}\n+ #end if\n+\n+ #if str( $additional_params.GO_enrichment.examine_GO_enrichment ) == "yes":\n+ --examine_GO_enrichment\n+ --GO_annots "${$additional_params.GO_enrichment.GO_annots}"\n+ --gene_lengths "${$additional_params.GO_enrichment.gene_lengths}"\n+ #end if\n+\n+ --output results\n+ ]]></command>\n+ <inputs>\n+ <param format="tabular" name="matrix" argument="--matrix" type="data" label="Expression matrix" help="Raw counts matrix produced by \'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity\' tool"/>\n+ <param format="tabular" name="samples" argument="--samples" type="data" label="Sample description" help="File describing samples and replicates"/>\n+ <param format="tabular" name="DE_results" type="data_collection" collection_type="list" label="Differential expression results"/>\n+ <param name="p" type="float" argument="-P" value="0.001" label="p-value cutoff for FDR"/>\n+ <param name="c" type="float" argument="-C" value="2" label="min abs(log2(a/b)) fold change" help="Default: 2 (meaning 2^(2) or 4-fold"/>\n+ <section name="additional_params" title="Additional Options" expanded="False">\n+ <param name="max_DE_genes_per_comparison" argument="--max_DE_genes_per_comparison" type="integer" value="" optional="true" label="Maximum differential expression genes per comparison" help="Extract only up to the top number of DE features within each pairwise comparison. This is useful when you have massive numbers of DE features but still want to make useful heatmaps and other plots with more manageable numbers of data points."/>\n+ <param name="order_columns_by_samples_file" argument="--order_columns_by_samples_file" type="boolean" checked="false" truevalue="--order_columns_by_samples_file" falsevalue="" label="Order columns by samples file" help="Instead of clustering samples or replicates hierarchically based on gene expression patterns, order columns according to order in the --samples file."/>\n+ <param name="max_genes_clust" argument="--max_genes_clust" type="integer" value="10000" label="Maximum genes in cluster" help="If more than 10000, heatmaps are not generated, since too time consuming"/>\n+ <conditional name="GO_enrichment">\n+ <param type="select" name="examine_GO_enrichment" argument="--examine_GO_enrichment" label="Run GO enrichment analysis" help="To examine GO enrichment, you must first run Trinotate and then extr'..b'nt name="results_matrix_log2" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.dat"/>\n+ <element name="results_matrix_log2_sample_cor" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.sample_cor.dat"/>\n+ <element name="results_matrix_log2_sample_cor_matrix" delta="100" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.sample_cor_matrix.pdf"/>\n+ </output_collection>\n+ <output name="rdata" compare="sim_size" file="count/analyze_diff_expr/results.matrix.RData"/>\n+ </test>\n+ <test>\n+ <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>\n+ <param name="samples" value="count/samples.txt"/>\n+ <param name="DE_results">\n+ <collection type="list">\n+ <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results" ftype="tabular" />\n+ <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />\n+ <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />\n+ </collection>\n+ </param>\n+ <section name="additional_params">\n+ <conditional name="GO_enrichment">\n+ <param name="examine_GO_enrichment" value="yes"/>\n+ <param name="GO_annots" value="count/trinotate/go_annotations.txt"/>\n+ <param name="gene_lengths" value="count/trinotate/genes.lengths.txt"/>\n+ </conditional>\n+ </section>\n+ <assert_command>\n+ <has_text text="--examine_GO_enrichment" />\n+ <has_text text="--GO_annots" />\n+ <has_text text="--gene_lengths" />\n+ </assert_command>\n+ <output_collection name="GOseq_enrichment">\n+ <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_37-UP.subset.GOseq.enriched" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched"/>\n+ </output_collection>\n+ </test>\n+ </tests>\n+ <help>\n+<![CDATA[\n+Trinity_ assembles transcript sequences from Illumina RNA-Seq data.\n+This tool extracts the transcripts that are most differentially expressed (most significant FDR and fold-changes), once differential expression analyses have been runned. \n+\n+**Inputs**\n+\n+This tool uses the raw counts matrix produced by \'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity\' tool.\n+\n+You must describe your samples and replicates with a tabular file looking like this:\n+\n+=========== ================\n+ConditionA CondA_replicate1\n+----------- ----------------\n+ConditionA CondA_replicate2\n+----------- ----------------\n+ConditionB CondB_replicate1\n+----------- ----------------\n+ConditionB CondB_replicate2\n+----------- ----------------\n+ConditionC CondC_replicate1\n+----------- ----------------\n+ConditionC CondC_replicate2\n+----------- ----------------\n+ConditionC CondC_replicate3\n+=========== ================\n+\n+This file can be generated with the \'Describe samples and replicates\' tool.\n+It will probably be the same file as used in the tool \'RNASeq samples quality check for transcript quantification\' or in the tool \'Differential expression analysis\'.\n+The names in column 2 must match the names given in the tool \'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity\'.\n+\n+You must also provide as a data collection the files resulting from the differential expression analysis (outputs of tool \'Differential expression analysis\').\n+\n+.. _Trinity: http://trinityrnaseq.github.io\n+]]>\n+ </help>\n+ <expand macro="citation" />\n+</tool>\n'

diff -r 000000000000 -r d4128a4e49ca macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,23 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2.2.0">trinity</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+
+    <token name="@WRAPPER_VERSION@">2.2.0</token>
+
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" level="fatal" description="Error in Trinity execution" />
+        </stdio>
+    </xml>
+
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1038/nbt.1883</citation>
+        </citations>
+    </xml>
+</macros>

diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,7 @@
+id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2
+TR4277|c0_g1_i1 3852.97388871986 161.116814813422 2007.04535176664 -4.57259674791206 0.121601866332754 -37.6030145409076 0 0 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00
+TR4761|c0_g1_i1 1645.20640957447 193.196157329029 919.201283451752 -3.08847487551254 0.143642016580712 -21.5011940728159 1.51733402752078e-102 1.66906743027286e-101 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00
+TR2107|c1_g1_i1 48.9228907410258 7.40521775805688 28.1640542495414 -2.6949883047084 0.431525668867458 -6.24525607429428 4.23106352657394e-10 1.55138995974378e-09 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00
+TR2672|c0_g1_i1 18.3155337236093 2.26581902751323 10.2906763755613 -2.88818323474529 0.724350842979802 -3.98727117216294 6.68376171815065e-05 0.000157545811927837 14.00 29.00 22.00 0.00 4.00 2.00 14.00 4.00 7.00
+TR127|c1_g1_i1 13.461799216177 1.21881296083961 7.34030608850831 -3.33218181130749 0.914685635912973 -3.64298036448506 0.000269499403689035 0.000576210779000196 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00
+TR5055|c0_g2_i1 23.3590211688541 5.52768338415684 14.4433522765055 -2.04478780320925 0.562727305023446 -3.63370994255211 0.00027937492315161 0.000576210779000196 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00

diff -r 000000000000 -r d4128a4e49ca 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.depleted Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,1 @@
+category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR under_represented_FDR

diff -r 000000000000 -r d4128a4e49ca 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,1 @@
+category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR

diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,4 @@
+id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2
+TR131|c0_g1_i1 26.1866396538608 1340.30918254958 683.247911101723 5.67372481552909 0.187406695960058 30.274931140872 2.45144211418965e-201 4.04487948841292e-200 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00
+TR3091|c0_g1_i1 16.7444693227929 328.569936894811 172.657203108802 4.29039998257063 0.240421038467916 17.8453599980735 3.14072644239509e-71 2.59109931497595e-70 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00
+TR3788|c0_g1_i1 19.5075441237117 134.95369713876 77.2306206312357 2.77038513264018 0.262760026053246 10.5434040871909 5.44900939296595e-26 2.56881871382681e-25 17.00 30.00 22.00 91.00 132.00 125.00 32.00 22.00 27.00

diff -r 000000000000 -r d4128a4e49ca 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset.GOseq.depleted Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,1 @@
+category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR under_represented_FDR

diff -r 000000000000 -r d4128a4e49ca 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset.GOseq.enriched Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,1 @@
+category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR

diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,7 @@
+id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2
+TR4277|c0_g1_i1 4705.34614971641 162.902721493704 2434.12443560506 -4.84860951090545 0.124597307945428 -38.9142397284305 0 0 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00
+TR4761|c0_g1_i1 2012.6141923276 384.620292965437 1198.61724264652 -2.38450946693381 0.143863830576436 -16.5747669680385 1.06073316501088e-61 1.34359534234711e-60 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00
+TR2107|c1_g1_i1 59.5986596731862 1.89840873462066 30.7485342039034 -4.81058600791914 0.641850436461167 -7.49487066557473 6.63637683134955e-14 2.29256654173894e-13 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00
+TR127|c1_g1_i1 16.3791628279609 1.58772512712498 8.98344397754296 -3.19771077466237 0.834376974262452 -3.83245328346816 0.00012687169720824 0.000267840249661839 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00
+TR1894|c2_g1_i1 16.2826445742552 1.67571344127509 8.97917900776516 -3.15659686337855 0.834779400611257 -3.7813545244015 0.00015597736029041 0.000307529893573321 21.00 14.00 11.00 1.00 2.00 5.00 1.00 3.00 1.00
+TR5055|c0_g2_i1 28.6665933385886 6.05959103586122 17.3630921872249 -2.17768048931004 0.577307428800381 -3.77213314894485 0.000161857838722801 0.000307529893573321 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00

diff -r 000000000000 -r d4128a4e49ca 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.depleted Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,1 @@
+category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR under_represented_FDR

diff -r 000000000000 -r d4128a4e49ca 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,2 @@
+category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR go_term
+GO:0008270 0.0469428206943769 0.996332779511344 3 6 zinc ion binding MF 0.790651800018629 MF zinc ion binding

diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,5 @@
+id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2
+TR131|c0_g1_i1 32.0461070493257 1436.30905989883 734.177583474076 5.48367743370229 0.196017912869615 27.9753893581648 3.23827538807456e-172 6.15272323734167e-171 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00
+TR3091|c0_g1_i1 20.4914097091341 321.651020117047 171.071214913091 3.96886910507283 0.256323110469072 15.4838519937191 4.45952081812589e-54 4.2365447772196e-53 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00
+TR2779|c0_g1_i1 191.51955185349 1058.15934185376 624.839446853626 2.46616535412611 0.177102083131526 13.9251064161374 4.4587691300744e-44 3.38866453885655e-43 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00
+TR5075|c0_g1_i1 19.3833722195684 136.98672801182 78.1850501156942 2.80049241151413 0.293976352213923 9.52625063350759 1.63066468983638e-21 8.85217974482605e-21 13.00 22.00 21.00 6.00 8.00 10.00 163.00 121.00 142.00

diff -r 000000000000 -r d4128a4e49ca 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.depleted Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,1 @@
+category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR under_represented_FDR

diff -r 000000000000 -r d4128a4e49ca 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.enriched Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,1 @@
+category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR

diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,1 @@
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diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset Mon Nov 21 11:59:35 2016 -0500

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diff -r 000000000000 -r d4128a4e49ca 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.depleted Mon Nov 21 11:59:35 2016 -0500

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diff -r 000000000000 -r d4128a4e49ca 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.enriched Mon Nov 21 11:59:35 2016 -0500

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diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/results.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/results.matrix.RData

Binary file test-data/count/analyze_diff_expr/results.matrix.RData has changed

diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/results.matrix.log2.centered.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/results.matrix.log2.centered.dat Mon Nov 21 11:59:35 2016 -0500

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diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/results.matrix.log2.centered.genes_vs_samples_heatmap.pdf

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diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/results.matrix.log2.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor.dat Mon Nov 21 11:59:35 2016 -0500

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diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor_matrix.pdf

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diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf

Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf has changed

diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,39 @@
+logFC logCPM PValue FDR
+TR131|c0_g1_i1 5.8364197685119 16.0402624962907 0 0
+TR4277|c0_g1_i1 -4.41329137350676 17.4523259866001 0 0
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+TR2487|c0_g1_i1 1.58705373680526 15.8895982491351 1.69098562804069e-123 1.28514907731092e-122
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diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf

Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf has changed

diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,39 @@
+logFC logCPM PValue FDR
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+TR2090|c0_g1_i1 2.22339391910091 8.98366602727699 0.254495907488744 0.322361482819076
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+TR3249|c0_g1_i1 0.258869539778469 7.31927198802943 0.798677928444158 0.820263818402108
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diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf

Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf has changed

diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,39 @@
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diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf

Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed

diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,39 @@
+logFC logCPM PValue FDR
+TR131|c0_g1_i1 5.83867709149149 16.0447742820606 3.67956255674e-64 1.3982337715612e-62
+TR3091|c0_g1_i1 4.35104356420213 13.9337836495047 7.47918124727105e-59 1.4210444369815e-57
+TR4277|c0_g1_i1 -4.51249642920563 17.4585638169146 1.30305812944242e-53 1.65054029729373e-52
+TR5075|c0_g1_i1 3.18286810352713 12.8084040893566 8.25600206225396e-24 7.84320195914126e-23
+TR2107|c1_g1_i1 -4.48477961203985 11.2510359028096 1.80754966502889e-22 1.37373774542196e-21
+TR2779|c0_g1_i1 2.75442228103487 15.7797198210508 8.23352696880425e-15 5.21456708024269e-14
+TR1891|c0_g1_i1 1.85607282303223 14.4424161372431 4.82341414399837e-12 2.61842482102769e-11
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+TR1479|c0_g1_i1 1.43256512308186 14.3771181295432 1.13197856555697e-09 4.77946505457389e-09
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diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf

Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed

diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,39 @@
+logFC logCPM PValue FDR
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+TR4277|c0_g1_i1 -4.47812345668175 17.3786096664403 1.7008141018303e-32 3.23154679347758e-31
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+TR1859|c3_g1_i1 2.08358066039446 6.92308482511994 0.0216139227266133 0.0357099592874481
+TR1492|c0_g1_i2 -0.80292474159496 16.7717103141256 0.00797659176853916 0.0150548881236999
+TR3638|c0_g1_i1 -0.765536214533451 15.2959378061905 0.00929698340782949 0.0160584258862509
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+TR1982|c2_g1_i1 1.06368641289493 9.64628067316551 0.0510418091524593 0.0745995672228252
+TR1837|c2_g1_i1 1.43890969571076 6.48444225997254 0.130037630852572 0.154419686637429
+TR5212|c0_g1_i1 0.63168831011067 12.8380836623566 0.0456316928604782 0.0693601731479268
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+TR1122|c0_g1_i1 -0.501746583160273 6.50836597017328 0.595453777887275 0.628534543325457
+TR3788|c0_g1_i1 0.524753873079964 11.0311382344715 0.215975804877357 0.234488016723988
+TR2278|c0_g1_i1 -0.424377145183038 15.1829447141358 0.145500439954072 0.167545961159234
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+TR2011|c5_g1_i1 0.0410416962762211 8.85697121679121 0.9477445647389 0.956400717774849

diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf

Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed

diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,40 @@
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+TR2011|c5_g1_i1 7.597917075274 4.42090354598533 6.00941031062966 -0.246737820349972 0.517913150509813 -0.476407714511773 0.633783939711306 1
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+TR2182|c3_g2_i6 1.29006258579706 1.76655578876639 1.52830918728173 0.209843639881372 0.537581597903129 0.390347513195914 0.696279593847798 1
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+TR1982|c2_g1_i1 5.5352448786851 10.687042573374 8.11114372602957 0.110416157924497 0.359967068804195 0.306739608962835 0.759041578558 0.9108498942696
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+TR131|c0_g1_i1 1275.67603302799 1312.2934796972 1293.9847563626 0.0343724958045096 0.405262489992082 0.0848153891695754 0.932408158838271 0.963782835492881
+TR5055|c0_g2_i1 5.17791343714095 5.60171771495863 5.38981557604979 0.043552763660028 0.53975688204026 0.0806895939805349 0.935688812631814 1
+TR939|c0_g1_i1 92.2508462008296 94.0990807885678 93.1749634946987 0.0253693962827489 0.353966153466169 0.0716718139130601 0.942863087697354 0.963782835492881
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diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf

Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed

diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,40 @@
+logFC logCPM PValue FDR
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diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf

Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed

diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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@@ -0,0 +1,40 @@
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diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf

Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed

diff -r 000000000000 -r d4128a4e49ca test-data/count/express_bowtie/results.xprs
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/results.xprs Mon Nov 21 11:59:35 2016 -0500

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diff -r 000000000000 -r d4128a4e49ca test-data/count/express_bowtie/results_B.xprs
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/results_B.xprs Mon Nov 21 11:59:35 2016 -0500

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diff -r 000000000000 -r d4128a4e49ca test-data/count/express_bowtie/sample_A
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/sample_A Mon Nov 21 11:59:35 2016 -0500

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diff -r 000000000000 -r d4128a4e49ca test-data/count/express_bowtie/sample_B
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_express_bowtie/matrix.TMM.EXPR.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_express_bowtie/matrix.TMM.EXPR.matrix Mon Nov 21 11:59:35 2016 -0500

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diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_express_bowtie/matrix.TPM.not_cross_norm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_express_bowtie/matrix.TPM.not_cross_norm Mon Nov 21 11:59:35 2016 -0500

diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_express_bowtie/matrix.counts.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_express_bowtie/matrix.counts.matrix Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,8 @@
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diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie/matrix.TMM.EXPR.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie/matrix.TMM.EXPR.matrix Mon Nov 21 11:59:35 2016 -0500

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diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie/matrix.TPM.not_cross_norm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie/matrix.TPM.not_cross_norm Mon Nov 21 11:59:35 2016 -0500

diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie/matrix.counts.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie/matrix.counts.matrix Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,8 @@
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diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie2/matrix.TMM.EXPR.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie2/matrix.TMM.EXPR.matrix Mon Nov 21 11:59:35 2016 -0500

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diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie2/matrix.TPM.not_cross_norm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie2/matrix.TPM.not_cross_norm Mon Nov 21 11:59:35 2016 -0500

diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie2/matrix.counts.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie2/matrix.counts.matrix Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,8 @@
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+TRINITY_DN2_c0_g1 0.00 0.00
+TRINITY_DN1_c0_g1 0.00 0.00
+TRINITY_DN2_c1_g1 6.00 1.00

diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm Mon Nov 21 11:59:35 2016 -0500

diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm.upper_quartile_norm.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm.upper_quartile_norm.matrix Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,8 @@
+RSEM RSEM.isoforms_B.results
+TRINITY_DN3_c2_g1_i1 524034.76 144812.45
+TRINITY_DN4_c0_g1_i1 0 0
+TRINITY_DN3_c3_g1_i1 0 0
+TRINITY_DN3_c1_g1_i1 144812.45 524034.76
+TRINITY_DN2_c0_g1_i1 0 0
+TRINITY_DN3_c0_g1_i1 0 0
+TRINITY_DN0_c0_g1_i1 331152.79 331152.79

diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.UpperQuartile.EXPR.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.UpperQuartile.EXPR.matrix Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,8 @@
+sample_A sample_B
+TRINITY_DN2_c0_g1 0 0
+TRINITY_DN1_c0_g1 329523.81 329523.81
+TRINITY_DN0_c0_g1 0 0
+TRINITY_DN2_c1_g1 145165.14 525311.05
+TRINITY_DN3_c0_g1 0 0
+TRINITY_DN2_c2_g1 525311.05 145165.14
+TRINITY_DN2_c3_g1 0 0

diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.counts.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.counts.matrix Mon Nov 21 11:59:35 2016 -0500

diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie_none/matrix.TPM.not_cross_norm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_none/matrix.TPM.not_cross_norm Mon Nov 21 11:59:35 2016 -0500

diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie_none/matrix.counts.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_none/matrix.counts.matrix Mon Nov 21 11:59:35 2016 -0500

diff -r 000000000000 -r d4128a4e49ca test-data/count/qcheck/input.matrix.CPM.log2.principal_components.pdf

Binary file test-data/count/qcheck/input.matrix.CPM.log2.principal_components.pdf has changed

diff -r 000000000000 -r d4128a4e49ca test-data/count/qcheck/input.matrix.CPM.log2.sample_cor_matrix.pdf

Binary file test-data/count/qcheck/input.matrix.CPM.log2.sample_cor_matrix.pdf has changed

diff -r 000000000000 -r d4128a4e49ca test-data/count/qcheck/matrix.counts.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/qcheck/matrix.counts.matrix Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,41 @@
+ wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2
+TR24|c0_g1_i1 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00
+TR2779|c0_g1_i1 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00
+TR127|c1_g1_i1 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00
+TR2107|c1_g1_i1 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00
+TR2011|c5_g1_i1 11.00 4.00 4.00 8.00 5.00 7.00 3.00 4.00 8.00
+TR4163|c0_g1_i1 368.00 422.00 425.00 172.00 216.00 210.00 234.00 254.00 212.00
+TR5055|c0_g2_i1 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00
+TR1449|c0_g1_i1 196.00 230.00 207.00 66.00 113.00 91.00 124.00 130.00 107.00
+TR1982|c2_g1_i1 7.00 7.00 6.00 4.00 3.00 8.00 16.00 9.00 11.00
+TR1859|c3_g1_i1 0.00 0.00 1.00 0.00 0.00 0.00 1.00 2.00 4.00
+TR1492|c0_g1_i2 1895.00 1906.00 1921.00 1104.00 1263.00 1319.00 899.00 929.00 922.00
+TR1122|c0_g1_i1 2.00 3.00 0.00 3.00 0.00 0.00 1.00 1.00 0.00
+TR2278|c0_g1_i1 497.00 610.00 598.00 333.00 406.00 413.00 323.00 409.00 337.00
+TR4084|c0_g1_i1 95.00 148.00 86.00 77.00 111.00 127.00 175.00 201.00 158.00
+TR4761|c0_g1_i1 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00
+TR3638|c0_g1_i1 647.00 676.00 712.00 117.00 184.00 174.00 324.00 344.00 338.00
+TR2090|c0_g1_i1 0.00 0.00 0.00 22.00 0.00 0.02 10.33 0.00 9.09
+TR3854|c0_g1_i1 1878.00 1734.00 1864.00 1775.00 2173.00 2151.00 2216.00 2142.00 2155.00
+TR131|c0_g1_i1 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00
+TR5075|c0_g1_i1 13.00 22.00 21.00 6.00 8.00 10.00 163.00 121.00 142.00
+TR2182|c3_g2_i6 1.44 2.70 3.84 3.35 0.00 0.00 1.22 2.18 2.63
+TR3788|c0_g1_i1 17.00 30.00 22.00 91.00 132.00 125.00 32.00 22.00 27.00
+TR4859|c0_g1_i1 6.00 12.00 8.00 4.00 1.00 3.00 1.00 1.00 2.00
+TR2487|c0_g1_i1 386.00 383.00 424.00 689.00 866.00 806.00 963.00 989.00 1032.00
+TR2122|c0_g2_i2 145.00 135.00 136.00 155.00 157.00 201.00 369.00 398.00 344.00
+TR4277|c0_g1_i1 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00
+TR4669|c0_g2_i1 0.00 0.00 0.00 209.00 0.00 217.50 0.14 0.06 0.18
+TR3091|c0_g1_i1 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00
+TR2130|c1_g3_i1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
+TR3807|c0_g1_i1 6.00 4.00 2.00 0.00 0.00 1.00 0.00 1.00 0.00
+TR1894|c2_g1_i1 21.00 14.00 11.00 1.00 2.00 5.00 1.00 3.00 1.00
+TR5212|c0_g1_i1 64.00 89.00 78.00 73.00 98.00 108.00 103.00 105.00 84.00
+TR939|c0_g1_i1 96.00 99.00 99.00 72.00 89.00 88.00 107.00 103.00 108.00
+TR1891|c0_g1_i1 115.00 137.96 124.00 96.53 139.00 110.94 364.77 411.00 384.00
+TR2672|c0_g1_i1 14.00 29.00 22.00 0.00 4.00 2.00 14.00 4.00 7.00
+TR2844|c0_g1_i1 166.00 211.00 178.00 161.00 214.00 223.00 199.00 245.00 213.00
+TR1837|c2_g1_i1 1.00 0.00 0.00 1.00 1.00 4.00 0.00 3.00 2.00
+TR1678|c0_g1_i1 1.00 0.00 1.00 0.00 0.00 2.00 8.00 10.00 6.00
+TR3249|c0_g1_i1 1.00 2.00 1.00 4.00 1.00 0.00 6.00 1.00 7.00
+TR1479|c0_g1_i1 136.00 178.00 141.00 277.00 324.00 354.00 367.00 363.00 302.00

diff -r 000000000000 -r d4128a4e49ca test-data/count/qcheck/wt_37.rep_compare.pdf

Binary file test-data/count/qcheck/wt_37.rep_compare.pdf has changed

diff -r 000000000000 -r d4128a4e49ca test-data/count/qcheck/wt_GSNO.rep_compare.pdf

Binary file test-data/count/qcheck/wt_GSNO.rep_compare.pdf has changed

diff -r 000000000000 -r d4128a4e49ca test-data/count/qcheck/wt_ph8.rep_compare.pdf

Binary file test-data/count/qcheck/wt_ph8.rep_compare.pdf has changed

diff -r 000000000000 -r d4128a4e49ca test-data/count/rsem_bowtie/RSEM.isoforms.results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/RSEM.isoforms.results Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,8 @@
+transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct
+TRINITY_DN0_c0_g1_i1 TRINITY_DN0_c0_g1 229 11.55 0.00 0.00 0.00 0.00
+TRINITY_DN1_c0_g1_i1 TRINITY_DN1_c0_g1 380 123.91 5.00 329523.81 3668378.58 100.00
+TRINITY_DN2_c0_g1_i1 TRINITY_DN2_c0_g1 279 35.45 0.00 0.00 0.00 0.00
+TRINITY_DN2_c1_g1_i1 TRINITY_DN2_c1_g1 541 281.27 5.00 145165.14 1616031.03 100.00
+TRINITY_DN2_c2_g1_i1 TRINITY_DN2_c2_g1 240 15.55 1.00 525311.05 5847953.22 100.00
+TRINITY_DN2_c3_g1_i1 TRINITY_DN2_c3_g1 202 3.45 0.00 0.00 0.00 0.00
+TRINITY_DN3_c0_g1_i1 TRINITY_DN3_c0_g1 216 6.82 0.00 0.00 0.00 0.00

diff -r 000000000000 -r d4128a4e49ca test-data/count/rsem_bowtie/RSEM.isoforms_B.results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/RSEM.isoforms_B.results Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,8 @@
+transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct
+TRINITY_DN0_c0_g1_i1 TRINITY_DN0_c0_g1 229 11.55 0.00 0.00 0.00 0.00
+TRINITY_DN1_c0_g1_i1 TRINITY_DN1_c0_g1 380 123.91 5.00 329523.81 3668378.58 100.00
+TRINITY_DN2_c0_g1_i1 TRINITY_DN2_c0_g1 279 35.45 0.00 0.00 0.00 0.00
+TRINITY_DN2_c2_g1_i1 TRINITY_DN2_c2_g1 541 281.27 5.00 145165.14 1616031.03 100.00
+TRINITY_DN2_c1_g1_i1 TRINITY_DN2_c1_g1 240 15.55 1.00 525311.05 5847953.22 100.00
+TRINITY_DN2_c3_g1_i1 TRINITY_DN2_c3_g1 202 3.45 0.00 0.00 0.00 0.00
+TRINITY_DN3_c0_g1_i1 TRINITY_DN3_c0_g1 216 6.82 0.00 0.00 0.00 0.00

diff -r 000000000000 -r d4128a4e49ca test-data/count/rsem_bowtie/sample_A
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/sample_A Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,8 @@
+gene_id transcript_id(s) length effective_length expected_count TPM FPKM
+TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 11.55 0.00 0.00 0.00
+TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 123.91 5.00 329523.81 3668378.58
+TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 35.45 0.00 0.00 0.00
+TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 541.00 281.27 5.00 145165.14 1616031.03
+TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 240.00 15.55 1.00 525311.05 5847953.22
+TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.45 0.00 0.00 0.00
+TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.82 0.00 0.00 0.00

diff -r 000000000000 -r d4128a4e49ca test-data/count/rsem_bowtie/sample_B
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/sample_B Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,8 @@
+gene_id transcript_id(s) length effective_length expected_count TPM FPKM
+TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 11.55 0.00 0.00 0.00
+TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 123.91 5.00 329523.81 3668378.58
+TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 35.45 0.00 0.00 0.00
+TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 541.00 281.27 5.00 145165.14 1616031.03
+TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 240.00 15.55 1.00 525311.05 5847953.22
+TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.45 0.00 0.00 0.00
+TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.82 0.00 0.00 0.00

diff -r 000000000000 -r d4128a4e49ca test-data/count/rsem_bowtie2/RSEM.isoforms.results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/RSEM.isoforms.results Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,8 @@
+transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct
+TRINITY_DN0_c0_g1_i1 TRINITY_DN0_c0_g1 229 10.58 0.00 0.00 0.00 0.00
+TRINITY_DN1_c0_g1_i1 TRINITY_DN1_c0_g1 380 122.00 5.00 309046.31 3415300.55 100.00
+TRINITY_DN2_c0_g1_i1 TRINITY_DN2_c0_g1 279 32.50 0.00 0.00 0.00 0.00
+TRINITY_DN2_c1_g1_i1 TRINITY_DN2_c1_g1 541 279.67 6.00 161779.66 1787842.67 100.00
+TRINITY_DN2_c2_g1_i1 TRINITY_DN2_c2_g1 240 14.25 1.00 529174.03 5847953.22 100.00
+TRINITY_DN2_c3_g1_i1 TRINITY_DN2_c3_g1 202 3.17 0.00 0.00 0.00 0.00
+TRINITY_DN3_c0_g1_i1 TRINITY_DN3_c0_g1 216 6.25 0.00 0.00 0.00 0.00

diff -r 000000000000 -r d4128a4e49ca test-data/count/rsem_bowtie2/RSEM.isoforms_B.results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/RSEM.isoforms_B.results Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,8 @@
+transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct
+TRINITY_DN0_c0_g1_i1 TRINITY_DN0_c0_g1 380 122.00 5.00 309046.31 3415300.55 100.00
+TRINITY_DN1_c0_g1_i1 TRINITY_DN1_c0_g1 229 10.58 0.00 0.00 0.00 0.00
+TRINITY_DN2_c0_g1_i1 TRINITY_DN2_c0_g1 279 32.50 0.00 0.00 0.00 0.00
+TRINITY_DN2_c2_g1_i1 TRINITY_DN2_c2_g1 541 279.67 6.00 161779.66 1787842.67 100.00
+TRINITY_DN2_c1_g1_i1 TRINITY_DN2_c1_g1 240 14.25 1.00 529174.03 5847953.22 100.00
+TRINITY_DN2_c3_g1_i1 TRINITY_DN2_c3_g1 202 3.17 0.00 0.00 0.00 0.00
+TRINITY_DN3_c0_g1_i1 TRINITY_DN3_c0_g1 216 6.25 0.00 0.00 0.00 0.00

diff -r 000000000000 -r d4128a4e49ca test-data/count/rsem_bowtie2/sample_A
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/sample_A Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,8 @@
+gene_id transcript_id(s) length effective_length expected_count TPM FPKM
+TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 10.58 0.00 0.00 0.00
+TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 122.00 5.00 309046.31 3415300.55
+TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 32.50 0.00 0.00 0.00
+TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 541.00 279.67 6.00 161779.66 1787842.67
+TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 240.00 14.25 1.00 529174.03 5847953.22
+TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.17 0.00 0.00 0.00
+TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.25 0.00 0.00 0.00

diff -r 000000000000 -r d4128a4e49ca test-data/count/rsem_bowtie2/sample_B
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/sample_B Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,8 @@
+gene_id transcript_id(s) length effective_length expected_count TPM FPKM
+TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 380.00 122.00 5.00 309046.31 3415300.55
+TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 229.00 10.58 0.00 0.00 0.00
+TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 32.50 0.00 0.00 0.00
+TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 541.00 279.67 6.00 161779.66 1787842.67
+TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 240.00 14.25 1.00 529174.03 5847953.22
+TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.17 0.00 0.00 0.00
+TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.25 0.00 0.00 0.00

diff -r 000000000000 -r d4128a4e49ca test-data/count/salmon/sample_A
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/salmon/sample_A Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,8 @@
+Name Length EffectiveLength TPM NumReads
+TRINITY_DN1_c0_g1_i1 380 120.403 179183 13
+TRINITY_DN0_c0_g1_i1 229 229 55271.5 7.62686
+TRINITY_DN2_c0_g1_i1 279 31.1522 565494 10.6151
+TRINITY_DN2_c1_g1_i1 541 278.129 113370 19
+TRINITY_DN2_c2_g1_i1 240 240 32900.7 4.75801
+TRINITY_DN2_c3_g1_i1 202 202 0 0
+TRINITY_DN3_c0_g1_i1 216 216 53781.8 7

diff -r 000000000000 -r d4128a4e49ca test-data/count/salmon/sample_B
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/salmon/sample_B Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,8 @@
+Name Length EffectiveLength TPM NumReads
+TRINITY_DN2_c2_g1 240.00 240.00 32900.70 4.76
+TRINITY_DN0_c0_g1 229.00 229.00 55271.50 7.63
+TRINITY_DN1_c0_g1 380.00 120.40 179183.00 13.00
+TRINITY_DN2_c0_g1 279.00 31.15 565494.00 10.62
+TRINITY_DN2_c3_g1 202.00 202.00 0.00 0.00
+TRINITY_DN3_c0_g1 216.00 216.00 53781.80 7.00
+TRINITY_DN2_c1_g1 541.00 278.13 113370.00 19.00

diff -r 000000000000 -r d4128a4e49ca test-data/count/samples.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/samples.txt Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,9 @@
+wt_37 wt_37_1 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_1-SRX707647-SRR1582649_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_1-SRX707647-SRR1582649_2.fastq
+wt_37 wt_37_2 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_2-SRX707648-SRR1582650_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_2-SRX707648-SRR1582650_2.fastq
+wt_37 wt_37_3 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_3-SRX707649-SRR1582651_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_3-SRX707649-SRR1582651_2.fastq
+wt_GSNO wt_GSNO_1 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_1-SRX707644-SRR1582646_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_1-SRX707644-SRR1582646_2.fastq
+wt_GSNO wt_GSNO_2 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_2-SRX707645-SRR1582647_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_2-SRX707645-SRR1582647_2.fastq
+wt_GSNO wt_GSNO_3 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_3-SRX707646-SRR1582648_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_3-SRX707646-SRR1582648_2.fastq
+wt_ph8 wt_ph8_1 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_1-SRX707641-SRR1582643_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_1-SRX707641-SRR1582643_2.fastq
+wt_ph8 wt_ph8_2 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_2-SRX707642-SRR1582644_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_2-SRX707642-SRR1582644_2.fastq
+wt_ph8 wt_ph8_3 /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_3-SRX707643-SRR1582645_1.fastq /broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_3-SRX707643-SRR1582645_2.fastq

diff -r 000000000000 -r d4128a4e49ca test-data/count/trinotate/genes.lengths.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/trinotate/genes.lengths.txt Mon Nov 21 11:59:35 2016 -0500

diff -r 000000000000 -r d4128a4e49ca test-data/count/trinotate/go_annotations.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/trinotate/go_annotations.txt Mon Nov 21 11:59:35 2016 -0500

b'@@ -0,0 +1,39 @@\n+TR24|c0_g1_i1\tGO: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\n+TR2779|c0_g1_i1\tGO: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\n+TR127|c1_g1_i1\tGO: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\n+TR2107|c1_g1_i1\tGO: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\n+TR2011|c5_g1_i1\tGO: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\n+TR4163|c0_g1_i1\tGO: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\n+TR5055|c0_g2_i1\tGO: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\n+TR1449|c0_g1_i1\tGO: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\n+TR1982|c2_g1_i1\tGO: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\n+TR1859|c3_g1_i1\tGO:0003676\n+TR1492|c0_g1_i2\tGO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229\n+TR1122|c0_g1_i1\tGO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234\n+TR2278|c0_g1_i1\tGO:0031090,GO:0033765\n+TR4084|c0_g1_i1\tGO:0003674,GO:0005488,GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043'..b'89,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\n+TR131|c0_g1_i1\tGO:0031090,GO:0033765\n+TR5075|c0_g1_i1\tGO:0031090,GO:0033765\n+TR2182|c3_g2_i6\tGO: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\n+TR3788|c0_g1_i1\tGO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229\n+TR4859|c0_g1_i1\tGO: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\n+TR2487|c0_g1_i1\tGO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169\n+TR2122|c0_g2_i2\tGO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872\n+TR4277|c0_g1_i1\tGO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872\n+TR3091|c0_g1_i1\tGO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169\n+TR2130|c1_g3_i1\tGO: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\n+TR3807|c0_g1_i1\tGO: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\n+TR1894|c2_g1_i1\tGO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872\n+TR5212|c0_g1_i1\tGO:0003865,GO:0005575,GO:0005783\n+TR939|c0_g1_i1\tGO: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\n+TR1891|c0_g1_i1\tGO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175\n+TR2672|c0_g1_i1\tGO:0003865,GO:0005575,GO:0005783\n+TR2844|c0_g1_i1\tGO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234\n+TR1837|c2_g1_i1\tGO: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\n+TR1678|c0_g1_i1\tGO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175\n+TR3249|c0_g1_i1\tGO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175\n+TR1479|c0_g1_i1\tGO: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\n'

diff -r 000000000000 -r d4128a4e49ca test-data/filtered/Trinity_filtered_exp.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filtered/Trinity_filtered_exp.fasta Mon Nov 21 11:59:35 2016 -0500

[

@@ -0,0 +1,34 @@
+>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT

diff -r 000000000000 -r d4128a4e49ca test-data/filtered/Trinity_filtered_pct_iso.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filtered/Trinity_filtered_pct_iso.fasta Mon Nov 21 11:59:35 2016 -0500

[

@@ -0,0 +1,45 @@
+>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA
+ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC
+AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG
+AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA
+AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
+GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
+TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
+TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT

diff -r 000000000000 -r d4128a4e49ca test-data/filtered/counts.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filtered/counts.matrix Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,8 @@
+ wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2
+TRINITY_DN1_c0_g1_i1 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00
+TRINITY_DN0_c0_g1_i1 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00
+TRINITY_DN2_c0_g1_i1 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00
+TRINITY_DN2_c1_g1_i1 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00
+TRINITY_DN2_c2_g1_i1 11.00 4.00 4.00 8.00 5.00 7.00 3.00 4.00 8.00
+TRINITY_DN2_c3_g1_i1 368.00 422.00 425.00 172.00 216.00 210.00 234.00 254.00 212.00
+TRINITY_DN3_c0_g1_i1 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00

diff -r 000000000000 -r d4128a4e49ca test-data/norm/Trinity.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/norm/Trinity.fasta Mon Nov 21 11:59:35 2016 -0500

[

@@ -0,0 +1,46 @@
+>TRINITY_DN1_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2]
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN0_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2]
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2]
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA
+ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC
+AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG
+AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA
+AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2]
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2]
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
+GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
+TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
+TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2]
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2]
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
+

diff -r 000000000000 -r d4128a4e49ca test-data/raw/Trinity.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw/Trinity.fasta Mon Nov 21 11:59:35 2016 -0500

[

@@ -0,0 +1,46 @@
+>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2]
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2]
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2]
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA
+ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC
+AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG
+AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA
+AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2]
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2]
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
+GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
+TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
+TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2]
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2]
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
+

diff -r 000000000000 -r d4128a4e49ca test-data/raw/map.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw/map.tsv Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,7 @@
+TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1
+TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1
+TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1
+TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1
+TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1
+TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1
+TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1

diff -r 000000000000 -r d4128a4e49ca test-data/reads.left.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.left.fq Mon Nov 21 11:59:35 2016 -0500

b'@@ -0,0 +1,400 @@\n+@61DFRAAXX100204:1:100:10494:3070/1\n+ACTGCATCCTGGAAAGAATCAATGGTGGCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTTT\n++\n+ACCCCCCCCCCCCCCCCCCCCCCCCCCCCCBC?CCCCCCCCC@@CACCCCCACCCCCCCCCCCCCCCCCCCCCCCC\n+@61DFRAAXX100204:1:100:10497:13422/1\n+GTAATTTCCGTACCTGCCACAGTGTGGGCTCACCCTGCTTAGAGGACAGGGAAGGACCCTAAAGGTAGGCTGATGC\n++\n+CCCCCCCCCCCCCCCCCCCCCCDCDCCCCCCCCCCCCCCCCCCCDDCCDDCDCBDCCDDDDBADDADDB@DBBBA@\n+@61DFRAAXX100204:1:100:10546:4478/1\n+CTGGGCTGCAGCTAAGTTCTCTGCATCCTCCTTCTTGCTTGTGGCTGGGAAGAAGACAATGTTGTCGATGGTCTGG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC7CB@CA:>AB?C=C@@@@?A@?5:88:\n+@61DFRAAXX100204:1:100:10609:6818/1\n+CACGTTTTCTAAGCAGTTTGTACCAGATCGTGCTAACTGCTCATTGTCTTGTTGTACACACCAGTAAAGCTGGGCA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@61DFRAAXX100204:1:100:10648:5988/1\n+TGCTCATTGTCTTGTTGTACACACCAGTAAAGCTGGGCAAAAATATCATCCAAAAGTACATCGCTGAGAACTCCTA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCDCCCCCCCCCCCCCCCCCCC\n+@61DFRAAXX100204:1:100:11486:13583/1\n+CCCACCTGAAAACATTTTCTACATCCACTGTTATATGGAATGCTTGATAAGCTTTTCATTCTAACCATCAGAGCAC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBC\n+@61DFRAAXX100204:1:100:1176:14271/1\n+TCTGAATAAGTCCTGCCACCAATGTTTTTCATAAGTGTGGCCATATGTTTTCATTATTTCAAACATTACTGTTAAG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCDCDCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCDBBABDB\n+@61DFRAAXX100204:1:100:12152:16425/1\n+CTCCGTTTTTTGAGAGTGCAACACATAGATACTGCTTGATAGCATTAATAAACATCTCATTTGTCCTGAAAACAGG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@61DFRAAXX100204:1:100:14680:13081/1\n+GCCTGAGTGTGCAAAAATCTTCAGAGTAAGAATACCATAGTTGCTAAATATCTTTTACCATGAGCAATAATTTTTT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC;CCCCCC\n+@61DFRAAXX100204:1:100:16086:14019/1\n+TCTGGTGCAGCTAGATGGAATACTGAGAAAATGTTCTTCCATCCTGAACGAATATTTGCAGCCTGAGAATTAACCA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCBCCDDCDCC\n+@61DFRAAXX100204:1:100:17458:1622/1\n+GTGAAAGGTCATCTATTTTAATGGCTTGTCTTTAAAAACCCTAAGAGAGGGAGGATGTCACAGGGAGGGCTTGTCA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCC5A###############################################\n+@61DFRAAXX100204:1:100:17716:21197/1\n+CCAGGCTTCCCGGTGACTTTCGGATGTTAGAGTGAGGAAGTAGCTCAGCGCTTCCCTGCAGACGTTTAAAAGCCTC\n++\n+CCCCCCCCCCCCCBCCCCCCCCC@CCCCCC@BBCCCCCCCBDB>CCCCAC@BCBBCDDBD@?BCBA@6BBB>;A;:\n+@61DFRAAXX100204:1:100:19734:13092/1\n+ATCATCTTGGAGACTTTTATCCACATCATGTGTTTGGGGCTCAAGATCCCCTTCATGCTCTTGGTTTATATGATCA\n++\n+;CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCDC\n+@61DFRAAXX100204:1:100:2082:1789/1\n+ACGGGTGTGGTGCCAAGCATCCCTTGTTCTTGGAGGTATTGTATTCCTCTCTTTGGTTTCTTATTAAATAAATCAA\n++\n+CCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCADCCCDBCCCCCCCCCCDABBCCDCC@CBBBDDDD;@B?=\n+@61DFRAAXX100204:1:100:2172:8797/1\n+GCCAAAACATAAGCAGTATCTGCACTAGCAAAAAGGGTTTGTCCTTGGTTGCACTCTAGGGATCTTGCAGCAAATT\n++\n+############################################################################\n+@61DFRAAXX100204:1:100:2238:12815/1\n+ACCATAGTTGCTAAATATCTTTTACCATGAGCAATAATTTTTTTCTCCCTTCCCCCACCCCCAATTATAAACATTT\n++\n+############################################################################\n+@61DFRAAXX100204:1:100:2327:5980/1\n+CTCCTAAATAATTTCCATCAGTGTGGGCCACCGTGATGAGTGTTTTTATTGTGTCGATATTCTTCTGTTTCATTTC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCC0BBBACCCBCCCCCC=CCCCCB@B@=DC@CCDDBCC-CC@CABBBB<CCCA\n+@61DFRAAXX100204:1:100:3665:17139/1\n+ATACTTCTTTGGGTAATTTCCGTACCTGCCACAGTGTGGGCTCACCCTGCTTAGAGGACAGGGAAGGACCCTAAAG\n++\n+CCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCDCBCCCCCCCCCCCCCCCCCCCCCCCCBCBCDCCCBDBA>DC\n+@61DFRAAXX100204:1:100:6480:5393/1\n+TGGAGACTTTTATCCACATCATGTGTTTGGGGCTCAAGATCCCCTTCATGCTCTTGGTTTATATGATCAACAGTCT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCBCCCCBDCBDDADBDC\n+@61DFRAAXX100204:1:100:8693:14085/1\n+AGCTATTTCGTTATAAATGGCTGATAGATACTCTTCAGGGAGATCTTTACTGTCATTGATACCACGATTCATTTTA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@61DFRAAXX100204:1:100:9306:14527/1\n+GTAGAATGATGCGTGAGCTT'..b'+\n+CCCCCCCCCCCCCBBBBBBCCCCCCCCCC?CCCCCCCCCCCCACCCCCCCCCCCCCCCCDCCDCCCCCCCACCBB@\n+@61DFRAAXX100204:1:103:13776:4298/1\n+TGATATTTGAAATACTATTCCAATTCGCAGGAAAAATCTTCTAAGAACAGCACGCAGTTCCGGAATCAAGTCAAAT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDC@BCC\n+@61DFRAAXX100204:1:103:13798:6365/1\n+GGTCACAGTCATAATTTACATAAATGTCCACCACACTCTGAGCATCTGCACAGATCCTTGTCAGTGTCTGAATAAC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCC\n+@61DFRAAXX100204:1:103:14748:1375/1\n+CCAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATCTACATCAAGCCCCGCCACCC\n++\n+CCCCCCCCCCCCCCCBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@BCCCCCCCCCACCCDBD@@DDB\n+@61DFRAAXX100204:1:103:16156:9928/1\n+CATGAGCAATAATTTTTTTCTCCCTTCCCCCACCCCCAATTATAAACATTTTATCCTTCAAAATACAGCTCTCCTG\n++\n+CCCCCCCCCCCCCCCCCCBBBBCCCCCCCCCC@B@BB@CCCCCCCCCACCCCCCCCCCCCAACCCCCCCCCCCCCC\n+@61DFRAAXX100204:1:103:16292:7311/1\n+CTGGTTCTTACATCTAATTTGCATCTATTGATGATACAAGACAACTCAAAGAGGATCGGGAACCACCCTCTCACCC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDBCDCDCCCCCCCCCCBDC\n+@61DFRAAXX100204:1:103:1757:15756/1\n+GGCAAAAATATCATCCAAAAGTACATCGCTGAGAACTTCTAAATACTGGGTGAATACATCACATATTGCATAAAGG\n++\n+CCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCC\n+@61DFRAAXX100204:1:103:19512:1223/1\n+CTGTTAAGCCCCTGGTTCTTACATCTAATTTGCATCTATTGATGATACAAGACAACTCAAAGAGGATCGGGAACCA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCDCCDADBB@C@BB@\n+@61DFRAAXX100204:1:103:2005:9846/1\n+TGCTTCCCTGCAGACGTTTAAAAGCCTCTGCTGGACTTCTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCBCCCCABDBBCBBDDDC\n+@61DFRAAXX100204:1:103:2755:14644/1\n+CTTACATCTAATTTGCATCTATTGATGATACAAGACAACTCAAAGAGGATCGGGAACCACCCTCTCACCCACACCC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC=C\n+@61DFRAAXX100204:1:103:3597:13520/1\n+GTTGTTGTGATGTTAAAAAGCGGTACATTCCTTGGTCTTGAGTATCAACTCGAACATCGAAGTCTACTACATCTCT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCDCCCCCCCCCCCCCCCCCDCBCCCCDADDCDCDC\n+@61DFRAAXX100204:1:103:4062:11566/1\n+GATGATACAAGACAACTCAAAGAGGATCGGGAACCACCCTCTCACCCACACCCTGTCTTCAGGTGCCACGCTCATG\n++\n+CCCCCCCCCCCCCBCCCCCCCCCCCCBCCCCC@CACCBCCCCCCCCCACCBCC=@BCBAC3;;-6AC@C@C?@:AB\n+@61DFRAAXX100204:1:103:5147:16732/1\n+CATGGTTACAAGTTGTTGTCATCCATTCAGCTTTCTCTGTCTGCTGTTCTGGCAATTTCATGTTGTCAAAGATTCT\n++\n+CCCCCCCCCC;????CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@61DFRAAXX100204:1:103:6646:12936/1\n+GTGCAACACATAGATACTGCTTGATAGCATTAATAAACATCTCATTTGTCCTGAAAACAGGTCCTGCATTCTGCAG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCDC\n+@61DFRAAXX100204:1:103:7220:15954/1\n+GAGGAATTGTGGTTTTGAAGATATCCAGGGTGCAGTTACACGTTTTATCCCAGATTTCAAGAGTAAACTTTTCACC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCABCCCCCCCA\n+@61DFRAAXX100204:1:103:7253:3680/1\n+CTTTACATCTGTACCATATACATATCCACCTGAAAACATTTTCTACATCCACTGTTATATGGAATGCTTGATAAGC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@61DFRAAXX100204:1:103:8055:11636/1\n+TTCCTGATGATGATGTGGATTCTAAGGAGTTTAAACTTCCATATCTGTTTATAGTCTCTGGGTGTTTAACTTCACT\n++\n+CCCCCCCCCCCCCCCCCC<CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCBCDCCCABCCCDCC\n+@61DFRAAXX100204:1:103:8348:14452/1\n+GTCAGAGCACAGTTCACAGTATGAATACATTTCCAGTAAATCTAACCTCCCAAAACCATGCCAGGTTTGTTATTTT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDBCCDCCCDCCCBCB\n+@61DFRAAXX100204:1:104:12460:3347/1\n+CTGATGCTGTGGGAACAGCCTTTCTGCTCAACATGAGCCCAACACGAGACAGAGGCCACTGGGTTACTAAAGGGAC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCC@CCDCDDCCCCBCCDCBB@BBAAB\n+@61DFRAAXX100204:1:104:12993:12947/1\n+GGTGAATACATCACATATTGCATAAAGGACATGGTTACAAGTTGTTGTCATCCATTCAGCTTTCTCTGTCTGCTGT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@61DFRAAXX100204:1:104:13501:6860/1\n+GTGATATTTGAAATACTATTCCAATTCGCAGGAAAAATCTTCTAAGAACAGCACGCAGTTCCGGAATCAAGTCAAA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCBCCCCCCACCCDCBCC>A\n'

diff -r 000000000000 -r d4128a4e49ca test-data/reads.right.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.right.fq Mon Nov 21 11:59:35 2016 -0500

b"@@ -0,0 +1,400 @@\n+@61DFRAAXX100204:1:100:10494:3070/2\n+CTCAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCATCTAGCTGC\n++\n+C<CCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCACCCCCACCC=\n+@61DFRAAXX100204:1:100:10497:13422/2\n+GAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCACCC\n+@61DFRAAXX100204:1:100:10546:4478/2\n+CTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@BCDCBCCCCCCCCCCCACCCCCCCCCBDC\n+@61DFRAAXX100204:1:100:10609:6818/2\n+AGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGCCCTTTATGCAATATGTGATGTATTCACCCA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?CBCC\n+@61DFRAAXX100204:1:100:10648:5988/2\n+AGATGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCACCCBCCBACC\n+@61DFRAAXX100204:1:100:11486:13583/2\n+CTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCBBBB@CCDCCCCDB@BDCCABCDDCBBCCCBC@\n+@61DFRAAXX100204:1:100:1176:14271/2\n+TGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCG\n++\n+CCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCDCCCCCCCCCC:BBBACCABC@CDDAB@DDCABDDABDBB\n+@61DFRAAXX100204:1:100:12152:16425/2\n+CCTTTCTAGTGTTCAGGTCATTGTGTAAGCTGTCAATGAAACCACTGTCAGATGGACCACCAGATCCAAAGTCTCA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCC=\n+@61DFRAAXX100204:1:100:14680:13081/2\n+CACAGCATCAGCCTACCTTTAGGGTCCTTCCCTGTCCTCTAAGCAGGGTGAGCCCACACTGTGGCAGGGACGGGAA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCDCCCCCCCCCBCCDCCB'299@'9@\n+@61DFRAAXX100204:1:100:16086:14019/2\n+AGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACGACCTTTTGAACATATAATGAAACGAAACAG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCBCCCCCC\n+@61DFRAAXX100204:1:100:17458:1622/2\n+AAAACATTTGGGTTGAACTTTTAGTCTTTGGGGGAGTGGTGGTCATTTTGAGGGCTTGCTGTGCCCTGAATCTGTT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@CCCCCBCCCCCCCDCCCDDCBDCBB@BABA=BBDB@AB<\n+@61DFRAAXX100204:1:100:17716:21197/2\n+GCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCAC?CCDBBCCBD@BCBBBB@B??BBA=@A?@\n+@61DFRAAXX100204:1:100:19734:13092/2\n+GGCTTTACTTACCGCAGTGACATCACAACACATAGAAATCCATGAAGGAACTGTGCTGCAAGCTGTGAGGACATGC\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCC?CC@CBCCCBCAACCC\n+@61DFRAAXX100204:1:100:2082:1789/2\n+GGAGCAAGGATCAGTATGTGAACCCCAACTCTCAAACTACCCTTGGTCAGGAAAAACCCTCAGAGCAAGAGATACG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCBCBCCCBCDBBDACCDBCDCA@B##\n+@61DFRAAXX100204:1:100:2172:8797/2\n+TATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAA\n++\n+############################################################################\n+@61DFRAAXX100204:1:100:2238:12815/2\n+CCCCTCCAGACCCTTTAGAAACCCAGAGGCCTCGGGCTCGCGTGTGGCTCATTTTCGCCAGAAAGGCGGTTCCCAC\n++\n+############################################################################\n+@61DFRAAXX100204:1:100:2327:5980/2\n+CAAGACTGTGATGATACTGAAGTAGCCTCTCTTTGCCTAGAAGGGATAAGATGTGCTATCAGGATTGCATGCATTT\n++\n+CCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCACCCC?BCCCCACBCCBCCCCCCCDDDAA@CCDBBC\n+@61DFRAAXX100204:1:100:3665:17139/2\n+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?CCCCCC@CC@@CB@@@@DABBBCBBB\n+@61DFRAAXX100204:1:100:6480:5393/2\n+TGCTACAATATCTATTTAGCCAGCAAAAATCTCATCAATCAGACAACAGCCAAAGCTACTCTTACTGAAATGCTGA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB\n+@61DFRAAXX100204:1:100:8693:14085/2\n+TGCAACCAAGGACAAACCCTTTTTGCTAGTGCAGATACTGCTTATGTTTTGGCCTACTCAATTATCATGTTGACTA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@61DFRAAXX100204:1:100:9306:14527/2\n+GCCTGGGAAGAAGTCCAGCA"..b'+\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCBCCCCCCCCDCCCDDCBCCCCB@BCC>\n+@61DFRAAXX100204:1:103:13776:4298/2\n+CCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCBCCCCCCCC\n+@61DFRAAXX100204:1:103:13798:6365/2\n+GTTTATTAATGCTATCAAGCAGTATCTATGTGTTGCACTCTCAAAAAACGGAGTCTCATCTGTTCCAGAGGTTTTT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCCCCCCDCCDDCDCCBDDC@\n+@61DFRAAXX100204:1:103:14748:1375/2\n+TAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTAAATACCCATA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@BCCB=CCBBBC@@CCCACCCACCCCBCCCDD>DC\n+@61DFRAAXX100204:1:103:16156:9928/2\n+CTCATGTTGAGCAGAAAGGCTGTTCCCACAGCATCAGCCTACCTTTAGGGTCCTTCCCTGTCCTCTAAGCAGGGTG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCDCCCDCCDCCA@ACBABB?B\n+@61DFRAAXX100204:1:103:16292:7311/2\n+CACCATTGATTCTTTCCAGGATGCAGTGAAGTGTTTGTCTGAATTCACATGTAATGCAGCTTTCCCAGACACAAGT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCC5CCCCDCCCCCBCCBCCCBDDDBDBBBBCD\n+@61DFRAAXX100204:1:103:1757:15756/2\n+TGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@61DFRAAXX100204:1:103:19512:1223/2\n+TGTCACTCTTGTATTTGAAAAACACTTTCCGGCCACCATTGATTCTTTCCAGGATGCAGTGAAGTGTTTGTCTGAA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCC@CBA8=A=CCACCCBCCA#\n+@61DFRAAXX100204:1:103:2005:9846/2\n+TTTAATTCCAACAATGAACAGAGGGCTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA\n++\n+CCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBDDBCDCCDBDCBCCDDDCDADBBDDC\n+@61DFRAAXX100204:1:103:2755:14644/2\n+GCTGCATCAGACCAAGATGAAAGCATAGTAGAACTTGCATTTCAGACAACAGGGCACATTGTCACTCTTGTATTTG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCACCCCC>CCC@CBACDCCDCC\n+@61DFRAAXX100204:1:103:3597:13520/2\n+CACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCACACDDCCDDCCB@A?B@BB@ABBBBADABD<?>AA\n+@61DFRAAXX100204:1:103:4062:11566/2\n+CAACAATTCGAGATATGGTTGTACGGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATG\n++\n+CCCCCCCBCCCCCCCCCCCCC?CCCC=CCCCCA=@A@CCACBCC?ABAABCCCCACC>BC<CCCACCCCB@C@B@?\n+@61DFRAAXX100204:1:103:5147:16732/2\n+GGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCBCCCBCCCCCCCBCCBBCCBC\n+@61DFRAAXX100204:1:103:6646:12936/2\n+CTCCAATGATACTCAGGAATCTGGAAATTCTTCAGGACCTTCACCTGGTGCTAAGTTTTCCCACATTTTACAAAAG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCC@CDCCDCCCCCDCCCDBDBADDC\n+@61DFRAAXX100204:1:103:7220:15954/2\n+GATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBCCCCCCCCCCCCCBCDC\n+@61DFRAAXX100204:1:103:7253:3680/2\n+GTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTT\n++\n+CCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@BCCCCCCCBCDCCCBCCCCCCB=CDA\n+@61DFRAAXX100204:1:103:8055:11636/2\n+AAATGACCTGTCGAAAATTGCACAAGGAAGGGGCAGCCAAGAACTTGGTATGAGTAATGTTCAGGAATTGAGCCTG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCDCCCCDACCCCCCCCCACCCCC\n+@61DFRAAXX100204:1:103:8348:14452/2\n+AACATTTGGGTTGAACTTTTAGTCTTTGGGGGAGTGGTGGTCATTTTGAGGGCTTGCTGTGCCCTGAATCTGTTGT\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@CCCCCDCCCCCCCCCCCCCACBCCDCCCCCAB@CBCCDCBB\n+@61DFRAAXX100204:1:104:12460:3347/2\n+CACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTTACATTG\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCBCCC@@@BBCCCACBCCC@ACBC\n+@61DFRAAXX100204:1:104:12993:12947/2\n+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTTGCCATTGTGCAAAA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCC@CCACBCDDCBCC,BBC?BBBBB@BBBD\n+@61DFRAAXX100204:1:104:13501:6860/2\n+CTGAGCTACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTA\n++\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCC\n'

diff -r 000000000000 -r d4128a4e49ca test-data/samples.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samples.tsv Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,4 @@
+ConditionA CondA_replicate1
+ConditionA CondA_replicate2
+ConditionB CondB_replicate1
+ConditionB CondB_replicate2

diff -r 000000000000 -r d4128a4e49ca tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon Nov 21 11:59:35 2016 -0500

@@ -0,0 +1,30 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="trinity" version="2.2.0">
+        <repository changeset_revision="76d63b5c571a" name="package_trinity_2_2_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bowtie" version="1.1.2">
+        <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bowtie2" version="2.2.6">
+        <repository changeset_revision="0d9cd7487cc9" name="package_bowtie_2_2_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bioconductor-edger" version="3.14.0">
+        <repository changeset_revision="5f4abad5b2c1" name="package_bioconductor_edger_3_14_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="rsem" version="1.2.28">
+        <repository changeset_revision="4567331d510a" name="package_rsem_1_2_28" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="eXpress" version="1.5.1">
+        <repository changeset_revision="93017e8743e5" name="package_express_1_5_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bioconductor-limma" version="3.28.10">
+        <repository changeset_revision="b313488c66bd" name="package_bioconductor_limma_3_28_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="deseq2" version="1.10.0">
+       <repository changeset_revision="e4a11a7d33d6" name="package_deseq2_1_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="TRINITY_MEM_OPTIONS">'--max_memory 30G --bflyHeapSpaceMax 30G'</environment_variable>
+    </set_environment>
+</tool_dependency>