Repository 'trinity_align_and_estimate_abundance'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/trinity_align_and_estimate_abundance

Changeset 0:a21e229da9a1 (2016-08-01)
Next changeset 1:a966877db15b (2016-11-18)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
added:
README.rst
align_and_estimate_abundance.xml
macros.xml
test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results
test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf
test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results
test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf
test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results
test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf
test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results
test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf
test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results
test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf
test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results
test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf
test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results
test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf
test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results
test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf
test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results
test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf
test-data/count/express_bowtie/results.xprs
test-data/count/express_bowtie/results.xprs.genes
test-data/count/express_bowtie/results_B.xprs
test-data/count/express_bowtie/results_B.xprs.genes
test-data/count/matrix_express_bowtie/matrix.TMM.EXPR.matrix
test-data/count/matrix_express_bowtie/matrix.TPM.not_cross_norm
test-data/count/matrix_express_bowtie/matrix.counts.matrix
test-data/count/matrix_rsem_bowtie/matrix.TMM.EXPR.matrix
test-data/count/matrix_rsem_bowtie/matrix.TPM.not_cross_norm
test-data/count/matrix_rsem_bowtie/matrix.counts.matrix
test-data/count/matrix_rsem_bowtie2/matrix.TMM.EXPR.matrix
test-data/count/matrix_rsem_bowtie2/matrix.TPM.not_cross_norm
test-data/count/matrix_rsem_bowtie2/matrix.counts.matrix
test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm
test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm.upper_quartile_norm.matrix
test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.UpperQuartile.EXPR.matrix
test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.counts.matrix
test-data/count/matrix_rsem_bowtie_none/matrix.TPM.not_cross_norm
test-data/count/matrix_rsem_bowtie_none/matrix.counts.matrix
test-data/count/qcheck/input.matrix.CPM.log2.principal_components.pdf
test-data/count/qcheck/input.matrix.CPM.log2.sample_cor_matrix.pdf
test-data/count/qcheck/matrix.counts.matrix
test-data/count/qcheck/wt_37.rep_compare.pdf
test-data/count/qcheck/wt_GSNO.rep_compare.pdf
test-data/count/qcheck/wt_ph8.rep_compare.pdf
test-data/count/rsem_bowtie/RSEM.genes.results
test-data/count/rsem_bowtie/RSEM.genes_B.results
test-data/count/rsem_bowtie/RSEM.isoforms.results
test-data/count/rsem_bowtie/RSEM.isoforms_B.results
test-data/count/rsem_bowtie2/RSEM.genes.results
test-data/count/rsem_bowtie2/RSEM.genes_B.results
test-data/count/rsem_bowtie2/RSEM.isoforms.results
test-data/count/rsem_bowtie2/RSEM.isoforms_B.results
test-data/count/salmon/quant.sf
test-data/count/salmon/quant.sf.genes
test-data/count/samples.txt
test-data/filtered/Trinity_filtered_exp.fasta
test-data/filtered/Trinity_filtered_pct_iso.fasta
test-data/filtered/counts.matrix
test-data/norm/Trinity.fasta
test-data/raw/Trinity.fasta
test-data/raw/map.tsv
test-data/reads.left.fq
test-data/reads.right.fq
tool_dependencies.xml
b
diff -r 000000000000 -r a21e229da9a1 README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Mon Aug 01 14:43:15 2016 -0400
b
@@ -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'
b
diff -r 000000000000 -r a21e229da9a1 align_and_estimate_abundance.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/align_and_estimate_abundance.xml Mon Aug 01 14:43:15 2016 -0400
[
b'@@ -0,0 +1,309 @@\n+<tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@.0">\n+    <description>on a de novo assembly of RNA-Seq data</description>\n+    <macros>\n+        <import>macros.xml</import>\n+    </macros>\n+    <expand macro="requirements">\n+        <requirement type="package" version="1.1.2">bowtie</requirement>\n+        <requirement type="package" version="2.2.6">bowtie2</requirement>\n+        <requirement type="package" version="1.2">samtools</requirement>\n+        <requirement type="package" version="1.2.28">rsem</requirement>\n+        <requirement type="package" version="1.5.1">eXpress</requirement>\n+        <requirement type="package" version="0.6.0">salmon</requirement>\n+    </expand>\n+    <expand macro="stdio"/>\n+    <command><![CDATA[\n+        ln -s \'$transcripts\' input.fa &&\n+\n+        #if $inputs.paired_or_single == "paired":\n+            #if $inputs.left_input.is_of_type(\'fasta\'):\n+                ln -s \'$inputs.left_input\' paired_left.fa &&\n+                ln -s \'$inputs.right_input\' paired_right.fa\n+            #else:\n+                ln -s \'$inputs.left_input\' paired_left.fq &&\n+                ln -s \'$inputs.right_input\' paired_right.fq\n+            #end if\n+        #else:\n+            #if $inputs.left_input.is_of_type(\'fasta\'):\n+                ln -s \'$inputs.input\' single.fa\n+            #else:\n+                ln -s \'$inputs.input\' single.fq\n+            #end if\n+        #end if\n+\n+        &&\n+\n+        align_and_estimate_abundance.pl\n+\n+        --transcripts input.fa\n+\n+        --est_method $method.est_method\n+        #if $method.est_method == "RSEM" or $method.est_method == "eXpress":\n+            --aln_method $method.aln_method\n+        #else if $method.est_method == "salmon":\n+            --salmon_idx_type $method.salmon_idx_type\n+        #end if\n+\n+        #if $inputs.paired_or_single == "paired":\n+\n+            #if $inputs.left_input.is_of_type(\'fasta\'):\n+                --left paired_left.fa --right paired_right.fa --seqType fa\n+            #else:\n+                --left paired_left.fq --right paired_right.fq --seqType fq\n+            #end if\n+\n+            #if $inputs.strand.is_strand_specific:\n+                --SS_lib_type $inputs.strand.library_type\n+            #end if\n+\n+            --max_ins_size $inputs.paired_fragment_length\n+\n+        #else:\n+            #if $inputs.input.is_of_type(\'fasta\'):\n+                --single single.fa --seqType fa\n+            #else:\n+                --single single.fq --seqType fq\n+            #end if\n+\n+            #if $inputs.strand.is_strand_specific:\n+                --SS_lib_type $inputs.strand.library_type\n+            #end if\n+        #end if\n+\n+        ## Additional parameters.\n+        #if $additional_params.gene_map.has_gene_map == "no":\n+            --gene_trans_map $additional_params.gene_map.gene_trans_map\n+        #else\n+            --trinity_mode\n+        #end if\n+\n+        --prep_reference\n+\n+        --output_dir output\n+\n+        ## CPU\n+        --thread_count \\${GALAXY_SLOTS:-4}\n+    ]]></command>\n+    <inputs>\n+        <param format="fasta" name="transcripts" argument="--transcripts" type="data" label="Transcripts" help="de novo assembly of RNA-Seq data"/>\n+        <conditional name="inputs">\n+            <param name="paired_or_single" type="select" label="Paired or Single-end data?">\n+                <option value="paired">Paired</option>\n+                <option value="single">Single</option>\n+            </param>\n+            <when value="paired">\n+                <param format="fasta,fastqsanger" name="left_input" argument="--left" type="data" label="Left/Forward strand reads" help=""/>\n+                <param format="fasta,fastqsanger" name="right_input" argument="--right" type="data" label="Right/Reverse strand reads" help=""/>\n+                <conditional name="strand">\n+                    <param name="is_strand_specific" type="boolean" checked="false" label="Strand'..b'ht.fq"/>\n+            <param name="transcripts" value="raw/Trinity.fasta"/>\n+            <param name="library_type" value="RF"/>\n+            <param name="est_method" value="RSEM"/>\n+            <param name="aln_method" value="bowtie2"/>\n+            <param name="has_gene_map" value="yes"/>\n+            <output name="isoforms_counts_rsem">\n+                <assert_contents>\n+                    <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />\n+                    <has_n_columns n="8" />\n+                </assert_contents>\n+            </output>\n+            <output name="genes_counts_rsem">\n+                <assert_contents>\n+                    <has_line_matching expression="TRINITY_DN0_c0_g1&#009;.*" />\n+                    <has_n_columns n="7" />\n+                </assert_contents>\n+            </output>\n+        </test>\n+        <test>\n+            <param name="paired_or_single" value="paired"/>\n+            <param name="left_input" value="reads.left.fq"/>\n+            <param name="right_input" value="reads.right.fq"/>\n+            <param name="transcripts" value="raw/Trinity.fasta"/>\n+            <param name="library_type" value="RF"/>\n+            <param name="est_method" value="eXpress"/>\n+            <param name="aln_method" value="bowtie"/>\n+            <param name="has_gene_map" value="yes"/>\n+            <output name="isoforms_counts_express">\n+                <assert_contents>\n+                    <has_line_matching expression=".*&#009;TRINITY_DN2_c3_g1_i1&#009;.*" />\n+                    <has_n_columns n="15" />\n+                </assert_contents>\n+            </output>\n+            <output name="genes_counts_express">\n+                <assert_contents>\n+                    <has_line_matching expression="NA&#009;TRINITY_DN3_c0_g1.*" />\n+                    <has_n_columns n="15" />\n+                </assert_contents>\n+            </output>\n+        </test>\n+        <test>\n+            <param name="paired_or_single" value="paired"/>\n+            <param name="left_input" value="reads.left.fq"/>\n+            <param name="right_input" value="reads.right.fq"/>\n+            <param name="transcripts" value="raw/Trinity.fasta"/>\n+            <param name="library_type" value="RF"/>\n+            <param name="est_method" value="salmon"/>\n+            <param name="aln_method" value="bowtie"/>\n+            <param name="has_gene_map" value="yes"/>\n+            <output name="isoforms_counts_salmon">\n+                <assert_contents>\n+                    <has_line_matching expression="TRINITY_DN2_c3_g1_i1&#009;.*" />\n+                    <has_n_columns n="5" />\n+                </assert_contents>\n+            </output>\n+            <output name="genes_counts_salmon">\n+                <assert_contents>\n+                    <has_line_matching expression="TRINITY_DN3_c0_g1.*" />\n+                    <has_n_columns n="5" />\n+                </assert_contents>\n+            </output>\n+        </test>\n+    </tests>\n+    <help>\n+<![CDATA[\n+Trinity_ assembles transcript sequences from Illumina RNA-Seq data.\n+This tool estimates the abundance of isoforms and genes of a transcriptome assembled with Trinity, using FastQ of a specific sample.\n+\n+**Inputs**\n+\n+It takes as input a transcriptome assembled with Trinity and the reads from a RNASeq sample.\n+You have to choose between several counting methods.\n+\n+If you dont align on a Trinity assembly, you need to provide a file of the following (tabular) format to map gene ids to transcript ids:\n+\n+=========== ================\n+gene1       transcript1\n+----------- ----------------\n+gene2       transcript2\n+=========== ================\n+\n+**Output**\n+\n+This tool will produce 2 tabular files, with counts for isoforms and genes respectively. More details on this page:\n+\n+.. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification\n+\n+\n+.. _Trinity: http://trinityrnaseq.github.io\n+]]>\n+    </help>\n+\n+    <expand macro="citation" />\n+</tool>\n'
b
diff -r 000000000000 -r a21e229da9a1 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Aug 01 14:43:15 2016 -0400
b
@@ -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>
b
diff -r 000000000000 -r a21e229da9a1 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
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results Mon Aug 01 14:43:15 2016 -0400
b
@@ -0,0 +1,39 @@
+id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj
+TR4277|c0_g1_i1 3852.97388871986 161.116814813422 2007.04535176664 -4.57259674791206 0.121601866332754 -37.6030145409076 0 0
+TR131|c0_g1_i1 26.1866396538608 1340.30918254958 683.247911101723 5.67372481552909 0.187406695960058 30.274931140872 2.45144211418965e-201 4.04487948841292e-200
+TR4761|c0_g1_i1 1645.20640957447 193.196157329029 919.201283451752 -3.08847487551254 0.143642016580712 -21.5011940728159 1.51733402752078e-102 1.66906743027286e-101
+TR3091|c0_g1_i1 16.7444693227929 328.569936894811 172.657203108802 4.29039998257063 0.240421038467916 17.8453599980735 3.14072644239509e-71 2.59109931497595e-70
+TR3638|c0_g1_i1 583.00358519031 183.754416330029 383.37900076017 -1.66018915730897 0.144484444213305 -11.4904352945982 1.47367477630653e-30 9.72625352362312e-30
+TR2487|c0_g1_i1 342.210853400436 920.407318992504 631.30908619647 1.42690938766606 0.124693202553469 11.4433614539188 2.5385551583546e-30 1.39620533709503e-29
+TR3788|c0_g1_i1 19.5075441237117 134.95369713876 77.2306206312357 2.77038513264018 0.262760026053246 10.5434040871909 5.44900939296595e-26 2.56881871382681e-25
+TR1479|c0_g1_i1 129.593534475689 371.064629188207 250.329081831948 1.51441163103673 0.145431922863633 10.4131995315551 2.1584296431011e-25 8.90352227779205e-25
+TR2107|c1_g1_i1 48.9228907410258 7.40521775805688 28.1640542495414 -2.6949883047084 0.431525668867458 -6.24525607429428 4.23106352657394e-10 1.55138995974378e-09
+TR3854|c0_g1_i1 1573.69549271337 2374.56159860719 1974.12854566028 0.593513416954248 0.111306645736399 5.33223701987958 9.70102011419466e-08 3.20133663768424e-07
+TR2122|c0_g2_i2 119.534640490118 199.143666337033 159.339153413576 0.738656537188098 0.168436715892782 4.38536534788702 1.15791268060543e-05 3.47373804181628e-05
+TR1449|c0_g1_i1 180.814952011467 104.755290736358 142.785121373912 -0.784194659361461 0.185749133486416 -4.2217944420118 2.42365089281258e-05 6.61949164163031e-05
+TR4163|c0_g1_i1 347.283468916919 232.772947466212 290.028208191566 -0.576744528291395 0.137147958253208 -4.20527243450891 2.60767852549073e-05 6.61949164163031e-05
+TR2672|c0_g1_i1 18.3155337236093 2.26581902751323 10.2906763755613 -2.88818323474529 0.724350842979802 -3.98727117216294 6.68376171815065e-05 0.000157545811927837
+TR127|c1_g1_i1 13.461799216177 1.21881296083961 7.34030608850831 -3.33218181130749 0.914685635912973 -3.64298036448506 0.000269499403689035 0.000576210779000196
+TR5055|c0_g2_i1 23.3590211688541 5.52768338415684 14.4433522765055 -2.04478780320925 0.562727305023446 -3.63370994255211 0.00027937492315161 0.000576210779000196
+TR2844|c0_g1_i1 158.206282615139 231.762548186068 194.984415400603 0.550641897280872 0.154759496937021 3.55804915484414 0.000373619406412113 0.000725261200682336
+TR5212|c0_g1_i1 65.7079302129484 107.875371765755 86.7916509893515 0.713884138135847 0.209708011296715 3.40418152707468 0.000663626354411326 0.00121664831642076
+TR1894|c2_g1_i1 13.3497721959996 2.96749216411516 8.15863218005739 -2.04982326482473 0.714661961266818 -2.8682417365424 0.00412760030232129 0.00716898999876856
+TR24|c0_g1_i1 69.9065207344592 41.2394742844514 55.5729975094553 -0.760369639593845 0.269117661787534 -2.8254170853868 0.00472191070589177 0.00779115266472142
+TR4669|c0_g2_i1 0 167.096667347181 83.5483336735905 4.37844609928899 2.00484514683835 2.18393231327309 0.0289672221614669 0.0455199205394479
+TR2779|c0_g1_i1 155.915506826481 205.619872596257 180.767689711369 0.402360429872658 0.188906223389576 2.12994798505331 0.0331759079102528 0.0497638618653791
+TR1492|c0_g1_i2 1640.89375005483 1435.64893261411 1538.27134133447 -0.192484740220531 0.101376439014472 -1.89871277874588 0.0576022504671541 0.0796285639028554
+TR3807|c0_g1_i1 3.48709246029019 0.350050334268211 1.9185713972792 -2.70461238638113 1.4262081182078 -1.89636586123194 0.0579116828384403 0.0796285639028554
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diff -r 000000000000 -r a21e229da9a1 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
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diff -r 000000000000 -r a21e229da9a1 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
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@@ -0,0 +1,39 @@
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diff -r 000000000000 -r a21e229da9a1 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
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+TR3091|c0_g1_i1 4.35104356420213 13.9337836495047 7.47918124727105e-59 1.4210444369815e-57
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+TR1891|c0_g1_i1 1.85607282303223 14.4424161372431 4.82341414399837e-12 2.61842482102769e-11
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diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
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@@ -0,0 +1,39 @@
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diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
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@@ -0,0 +1,40 @@
+id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj
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diff -r 000000000000 -r a21e229da9a1 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
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@@ -0,0 +1,40 @@
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diff -r 000000000000 -r a21e229da9a1 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
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results Mon Aug 01 14:43:15 2016 -0400
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@@ -0,0 +1,40 @@
+logFC logCPM PValue FDR
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diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
b
@@ -0,0 +1,8 @@
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+5 TRINITY_DN2_c1_g1_i1 541 259.008053 5 5 5.000000 10.443691 0.000000e00 0.000000e00 1.754947e06 1.754947e06 1.754947e06 T 2.788088e+05
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+7 TRINITY_DN3_c0_g1_i1 216 0.000000 0 0 0.000000 0.000000 0.000000e00 0.000000e00 0.000000e00 0.000000e00 0.000000e00 F 0.000000e+00
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diff -r 000000000000 -r a21e229da9a1 test-data/count/express_bowtie/results.xprs.genes
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/results.xprs.genes Mon Aug 01 14:43:15 2016 -0400
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@@ -0,0 +1,8 @@
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diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
b
@@ -0,0 +1,8 @@
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diff -r 000000000000 -r a21e229da9a1 test-data/count/express_bowtie/results_B.xprs.genes
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/results_B.xprs.genes Mon Aug 01 14:43:15 2016 -0400
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@@ -0,0 +1,8 @@
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+NA TRINITY_DN2_c2_g1 541.00 259.01 NA NA NA 10.44 NA NA 1754947.00 NA NA NA 278808.8
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diff -r 000000000000 -r a21e229da9a1 test-data/count/matrix_express_bowtie/matrix.TMM.EXPR.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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@@ -0,0 +1,8 @@
+ sample_A.tsv sample_B.tsv
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+TRINITY_DN2_c2_g1_i1 60178.11 278808.8
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diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
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@@ -0,0 +1,8 @@
+ sample_A.tsv sample_B.tsv
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+TRINITY_DN1_c0_g1_i1 0 0
+TRINITY_DN2_c2_g1_i1 60178.11 278808.8
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diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
b
@@ -0,0 +1,8 @@
+ sample_A.tsv sample_B.tsv
+TRINITY_DN2_c1_g1_i1 10.443691 1.000000
+TRINITY_DN1_c0_g1_i1 0.000000 0.000000
+TRINITY_DN2_c2_g1_i1 1.000000 10.443691
+TRINITY_DN2_c0_g1_i1 0.000000 0.000000
+TRINITY_DN3_c0_g1_i1 0.000000 0.000000
+TRINITY_DN2_c3_g1_i1 0.000000 0.000000
+TRINITY_DN0_c0_g1_i1 17.391774 17.391774
b
diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
b
@@ -0,0 +1,8 @@
+ sample_A.tsv sample_B.tsv
+TRINITY_DN3_c0_g1 0 0
+TRINITY_DN4_c0_g1 0 0
+TRINITY_DN0_c0_g1 331152.79 331152.79
+TRINITY_DN2_c0_g1 0 0
+TRINITY_DN3_c2_g1 524034.76 144812.45
+TRINITY_DN3_c1_g1 144812.45 524034.76
+TRINITY_DN3_c3_g1 0 0
b
diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
b
@@ -0,0 +1,8 @@
+ sample_A.tsv sample_B.tsv
+TRINITY_DN3_c0_g1 0 0
+TRINITY_DN4_c0_g1 0 0
+TRINITY_DN0_c0_g1 331152.79 331152.79
+TRINITY_DN2_c0_g1 0 0
+TRINITY_DN3_c2_g1 524034.76 144812.45
+TRINITY_DN3_c1_g1 144812.45 524034.76
+TRINITY_DN3_c3_g1 0 0
b
diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
b
@@ -0,0 +1,8 @@
+ sample_A.tsv sample_B.tsv
+TRINITY_DN3_c0_g1 0 0
+TRINITY_DN4_c0_g1 0 0
+TRINITY_DN0_c0_g1 331152.79 331152.79
+TRINITY_DN2_c0_g1 0 0
+TRINITY_DN3_c2_g1 524034.76 144812.45
+TRINITY_DN3_c1_g1 144812.45 524034.76
+TRINITY_DN3_c3_g1 0 0
b
diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
b
@@ -0,0 +1,8 @@
+ sample_A.tsv sample_B.tsv
+TRINITY_DN3_c0_g1 0 0
+TRINITY_DN4_c0_g1 0 0
+TRINITY_DN0_c0_g1 331152.79 331152.79
+TRINITY_DN2_c0_g1 0 0
+TRINITY_DN3_c2_g1 524034.76 144812.45
+TRINITY_DN3_c1_g1 144812.45 524034.76
+TRINITY_DN3_c3_g1 0 0
b
diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 test-data/count/qcheck/input.matrix.CPM.log2.principal_components.pdf
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diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
b
@@ -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
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+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
b
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b
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b
diff -r 000000000000 -r a21e229da9a1 test-data/count/rsem_bowtie/RSEM.genes.results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/RSEM.genes.results Mon Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 test-data/count/rsem_bowtie/RSEM.genes_B.results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/RSEM.genes_B.results Mon Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 test-data/count/rsem_bowtie2/RSEM.genes.results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/RSEM.genes.results Mon Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 test-data/count/rsem_bowtie2/RSEM.genes_B.results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/RSEM.genes_B.results Mon Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 test-data/count/salmon/quant.sf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/salmon/quant.sf Mon Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 test-data/count/salmon/quant.sf.genes
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/salmon/quant.sf.genes Mon Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 test-data/count/samples.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/samples.txt Mon Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
[
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 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 Aug 01 14:43:15 2016 -0400
[
@@ -0,0 +1,45 @@
+>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA
+ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC
+AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG
+AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA
+AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
+GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
+TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
+TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
b
diff -r 000000000000 -r a21e229da9a1 test-data/filtered/counts.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filtered/counts.matrix Mon Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 test-data/norm/Trinity.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/norm/Trinity.fasta Mon Aug 01 14:43:15 2016 -0400
[
@@ -0,0 +1,46 @@
+>TRINITY_DN1_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2]
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN0_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2]
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2]
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA
+ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC
+AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG
+AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA
+AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2]
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2]
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
+GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
+TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
+TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2]
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2]
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
+
b
diff -r 000000000000 -r a21e229da9a1 test-data/raw/Trinity.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw/Trinity.fasta Mon Aug 01 14:43:15 2016 -0400
[
@@ -0,0 +1,46 @@
+>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2]
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2]
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2]
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA
+ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC
+AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG
+AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA
+AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2]
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2]
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
+GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
+TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
+TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2]
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2]
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
+
b
diff -r 000000000000 -r a21e229da9a1 test-data/raw/map.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw/map.tsv Mon Aug 01 14:43:15 2016 -0400
b
@@ -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
b
diff -r 000000000000 -r a21e229da9a1 test-data/reads.left.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.left.fq Mon Aug 01 14:43:15 2016 -0400
b
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'
b
diff -r 000000000000 -r a21e229da9a1 test-data/reads.right.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.right.fq Mon Aug 01 14:43:15 2016 -0400
b
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'
b
diff -r 000000000000 -r a21e229da9a1 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon Aug 01 14:43:15 2016 -0400
b
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="trinity" version="2.2.0">
+        <repository changeset_revision="729219ec7049" 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="samtools" version="1.2">
+        <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bioconductor-edger" version="3.14.0">
+        <repository changeset_revision="8ed6cfd2b21f" 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="fc78b4bbe0ab" 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>