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Changeset 0:acff96adcbec (2016-12-13)

Next changeset 1:e4f348d88ae7 (2017-03-23)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit b9a2194247d728ef4d5a3c5511aa6ea63e9b2bcb

diff -r 000000000000 -r acff96adcbec README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Tue Dec 13 14:43:00 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 acff96adcbec define_clusters_by_cutting_tree.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/define_clusters_by_cutting_tree.xml Tue Dec 13 14:43:00 2016 -0500

[

@@ -0,0 +1,92 @@
+<tool id="trinity_define_clusters_by_cutting_tree" name="Partition genes into expression clusters" version="@WRAPPER_VERSION@.0">
+    <description>after differential expression analysis using a Trinity assembly</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="2.30.0">bioconductor-biobase</requirement>
+    </expand>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+
+        define_clusters_by_cutting_tree.pl
+
+        -R '${rdata}'
+
+        #if str( $method.method_selector ) == "--Ptree":
+            --Ptree ${method.ptree}
+        #else
+            #if str( $method.method_selector ) == "--Ktree":
+                --Ktree ${method.ktree}
+            #else
+                -K ${method.k}
+            #end if
+        #end if
+
+        $additional_params.column_ordering
+
+        &&
+        mv *.clusters_fixed_*/* .
+
+    ]]></command>
+    <inputs>
+        <param format="RData" name="rdata" argument="-R" type="data" label="RData file" help="RData file produced by 'Extract and cluster differentially expressed transcripts from a Trinity assembly' tool"/>
+        <conditional name="method">
+            <param name="method_selector" type="select" label="Method for partitioning genes into clusters">
+                <option value="--Ptree">Cut tree based on x percent of max(height) of tree</option>
+                <option value="--Ktree">Cut tree into K clusters</option>
+                <option value="-K">Define K clusters via k-means algorithm</option>
+            </param>
+            <when value="--Ptree">
+                <param name="ptree" type="float" argument="--Ptree" value="20" label="Cut tree based on this percent of max(height) of tree" help="Give a percent value"/>
+            </when>
+            <when value="--Ktree">
+                <param name="ktree" type="integer" argument="--Ktree" value="2" label="Cut tree into K clusters "/>
+            </when>
+            <when value="-K">
+                <param name="k" type="integer" argument="-K" value="2" label="Define K clusters via k-means algorithm" help="This does not leverage the already hierarchically clustered genes, and instead uses a least-sum-of-squares method to define exactly k gene clusters."/>
+            </when>
+        </conditional>
+        <section name="additional_params" title="Additional Options" expanded="False">
+            <param name="column_ordering" type="select" label="Column ordering in expression matrices" argument="--no_column_reordering / --lexical_column_ordering">
+                <option value="">Order based on sample clustering</option>
+                <option value="--no_column_reordering">No reordering based on sample clustering</option>
+                <option value="--lexical_column_ordering">Reorder column names according to lexical ordering</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="expression_matrices" type="list" label="${tool.name} on ${on_string}: expression matrices for each cluster">
+            <discover_datasets pattern="(?P<name>.+_log2_medianCentered_fpkm\.matrix)$" ext="tabular" />
+        </collection>
+        <data format="pdf" name="cluster_plots" label="${tool.name} on ${on_string}: cluster plots" from_work_dir="my_cluster_plots.pdf"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="rdata" value="count/analyze_diff_expr/results.matrix.RData"/>
+            <conditional name="method">
+                <param name="method_selector" value="--Ptree"/>
+                <param name="ptree" value="60"/>
+            </conditional>
+            <output_collection name="expression_matrices">
+                <element name="subcluster_1_log2_medianCentered_fpkm.matrix" compare="sim_size" file="count/define_clusters_by_cutting_tree/subcluster_1_log2_medianCentered_fpkm.matrix"/>
+                <element name="subcluster_2_log2_medianCentered_fpkm.matrix" compare="sim_size" file="count/define_clusters_by_cutting_tree/subcluster_2_log2_medianCentered_fpkm.matrix"/>
+            </output_collection>
+            <output name="rdata" delta="100" compare="sim_size" file="count/define_clusters_by_cutting_tree/my_cluster_plots.pdf"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
+This tool partitions the differentially expressed genes into gene clusters with similar expression patterns by one of several available methods, once differential expression analyses have been runned. It is a companion tool for the tool 'Extract and cluster differentially expressed transcripts from a Trinity assembly'.
+
+**Inputs**
+
+This tool uses the RData file produced by 'Extract and cluster differentially expressed transcripts from a Trinity assembly' tool.
+
+.. _Trinity: http://trinityrnaseq.github.io
+]]>
+    </help>
+
+    <expand macro="citation" />
+</tool>

diff -r 000000000000 -r acff96adcbec macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

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

diff -r 000000000000 -r acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

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

diff -r 000000000000 -r acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

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

diff -r 000000000000 -r acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

@@ -0,0 +1,1 @@
+id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2

diff -r 000000000000 -r acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

@@ -0,0 +1,3 @@
+id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2
+TR2779|c0_g1_i1 195.849684476753 966.924129135581 581.386906806167 2.25621220756415 0.156114979193812 14.4522467940961 2.42639762934434e-47 5.82335431042642e-46 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00
+TR24|c0_g1_i1 39.3724575919554 183.288101009647 111.330279300801 2.11680322693425 0.240338854880295 8.80757806717753 1.27878744153922e-18 7.67272464923531e-18 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00

diff -r 000000000000 -r acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

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diff -r 000000000000 -r acff96adcbec 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 acff96adcbec test-data/count/analyze_diff_expr/results.matrix.RData

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diff -r 000000000000 -r acff96adcbec test-data/count/analyze_diff_expr/results.matrix.log2.centered.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r acff96adcbec test-data/count/analyze_diff_expr/results.matrix.log2.centered.genes_vs_samples_heatmap.pdf

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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r acff96adcbec test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r acff96adcbec test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor_matrix.pdf

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diff -r 000000000000 -r acff96adcbec test-data/count/define_clusters_by_cutting_tree/my_cluster_plots.pdf

Binary file test-data/count/define_clusters_by_cutting_tree/my_cluster_plots.pdf has changed

diff -r 000000000000 -r acff96adcbec test-data/count/define_clusters_by_cutting_tree/subcluster_1_log2_medianCentered_fpkm.matrix
--- /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 Tue Dec 13 14:43:00 2016 -0500

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diff -r 000000000000 -r acff96adcbec test-data/count/define_clusters_by_cutting_tree/subcluster_2_log2_medianCentered_fpkm.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r acff96adcbec test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results
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diff -r 000000000000 -r acff96adcbec 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 acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

@@ -0,0 +1,39 @@
+logFC logCPM PValue FDR
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+TR4277|c0_g1_i1 -4.41329137350676 17.4523259866001 0 0
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diff -r 000000000000 -r acff96adcbec 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 acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

@@ -0,0 +1,39 @@
+logFC logCPM PValue FDR
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diff -r 000000000000 -r acff96adcbec 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 acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

@@ -0,0 +1,39 @@
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diff -r 000000000000 -r acff96adcbec 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 acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

@@ -0,0 +1,39 @@
+logFC logCPM PValue FDR
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+TR3091|c0_g1_i1 4.35104356420213 13.9337836495047 7.47918124727105e-59 1.4210444369815e-57
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diff -r 000000000000 -r acff96adcbec 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 acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

@@ -0,0 +1,39 @@
+logFC logCPM PValue FDR
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+TR2011|c5_g1_i1 0.0410416962762211 8.85697121679121 0.9477445647389 0.956400717774849

diff -r 000000000000 -r acff96adcbec 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 acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

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diff -r 000000000000 -r acff96adcbec test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf

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diff -r 000000000000 -r acff96adcbec test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf

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diff -r 000000000000 -r acff96adcbec test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results
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diff -r 000000000000 -r acff96adcbec test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf

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diff -r 000000000000 -r acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

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diff -r 000000000000 -r acff96adcbec test-data/count/express_bowtie/results_B.xprs
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r acff96adcbec test-data/count/express_bowtie/sample_A
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r acff96adcbec 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 acff96adcbec test-data/count/matrix_express_bowtie/matrix.TMM.EXPR.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r acff96adcbec test-data/count/matrix_express_bowtie/matrix.TPM.not_cross_norm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r acff96adcbec test-data/count/matrix_express_bowtie/matrix.counts.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r acff96adcbec test-data/count/matrix_rsem_bowtie/matrix.TMM.EXPR.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

diff -r 000000000000 -r acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

@@ -0,0 +1,8 @@
+ sample_A.tsv sample_B.tsv
+TRINITY_DN3_c0_g1 0.00 0.00
+TRINITY_DN4_c0_g1 0.00 0.00
+TRINITY_DN0_c0_g1 5.00 5.00
+TRINITY_DN2_c0_g1 0.00 0.00
+TRINITY_DN3_c2_g1 1.00 5.00
+TRINITY_DN3_c1_g1 5.00 1.00
+TRINITY_DN3_c3_g1 0.00 0.00

diff -r 000000000000 -r acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

@@ -0,0 +1,8 @@
+ sample_A.tsv sample_B.tsv
+TRINITY_DN3_c0_g1 0 0
+TRINITY_DN2_c2_g1 529174.03 161779.66
+TRINITY_DN2_c3_g1 0 0
+TRINITY_DN0_c0_g1 309046.31 309046.31
+TRINITY_DN2_c0_g1 0 0
+TRINITY_DN1_c0_g1 0 0
+TRINITY_DN2_c1_g1 161779.66 529174.03

diff -r 000000000000 -r acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

diff -r 000000000000 -r acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

@@ -0,0 +1,8 @@
+ sample_A.tsv sample_B.tsv
+TRINITY_DN3_c0_g1 0.00 0.00
+TRINITY_DN2_c2_g1 1.00 6.00
+TRINITY_DN2_c3_g1 0.00 0.00
+TRINITY_DN0_c0_g1 5.00 5.00
+TRINITY_DN2_c0_g1 0.00 0.00
+TRINITY_DN1_c0_g1 0.00 0.00
+TRINITY_DN2_c1_g1 6.00 1.00

diff -r 000000000000 -r acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

diff -r 000000000000 -r acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

diff -r 000000000000 -r acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

diff -r 000000000000 -r acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

diff -r 000000000000 -r acff96adcbec 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 acff96adcbec 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 acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 acff96adcbec 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 acff96adcbec 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 acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec test-data/count/salmon/sample_A
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/salmon/sample_A Tue Dec 13 14:43:00 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 acff96adcbec test-data/count/salmon/sample_B
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/salmon/sample_B Tue Dec 13 14:43:00 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 acff96adcbec test-data/count/samples.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/samples.txt Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 2016 -0500

diff -r 000000000000 -r acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec 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 Tue Dec 13 14:43:00 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 acff96adcbec test-data/filtered/counts.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filtered/counts.matrix Tue Dec 13 14:43:00 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 acff96adcbec test-data/norm/Trinity.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/norm/Trinity.fasta Tue Dec 13 14:43:00 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 acff96adcbec test-data/raw/Trinity.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw/Trinity.fasta Tue Dec 13 14:43:00 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 acff96adcbec test-data/raw/map.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw/map.tsv Tue Dec 13 14:43:00 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 acff96adcbec test-data/reads.left.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.left.fq Tue Dec 13 14:43:00 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 acff96adcbec test-data/reads.right.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.right.fq Tue Dec 13 14:43:00 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 acff96adcbec test-data/samples.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samples.tsv Tue Dec 13 14:43:00 2016 -0500

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

diff -r 000000000000 -r acff96adcbec tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Dec 13 14:43:00 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>