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

Changeset 0:64094e19077d (2018-06-14)
Next changeset 1:15f60c2e2d78 (2018-08-23)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
added:
README.rst
macros.xml
super_transcripts.xml
test-data/count/Trinity.map
test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset
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
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
test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset
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
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
test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset
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
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
test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset
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
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
test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.DE.subset.GOseq.enriched
test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset
test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset
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
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
test-data/count/analyze_diff_expr/results.matrix
test-data/count/analyze_diff_expr/results.matrix.RData
test-data/count/analyze_diff_expr/results.matrix.log2.centered.dat
test-data/count/analyze_diff_expr/results.matrix.log2.centered.genes_vs_samples_heatmap.pdf
test-data/count/analyze_diff_expr/results.matrix.log2.dat
test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor.dat
test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor_matrix.pdf
test-data/count/contig_exn50_statistic/ExN50.stats
test-data/count/contig_exn50_statistic/Trinity.fasta
test-data/count/contig_exn50_statistic/matrix.TMM.EXPR.matrix
test-data/count/define_clusters_by_cutting_tree/my_cluster_plots.pdf
test-data/count/define_clusters_by_cutting_tree/subcluster_1_log2_medianCentered_fpkm.matrix
test-data/count/define_clusters_by_cutting_tree/subcluster_2_log2_medianCentered_fpkm.matrix
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.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset
test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset
test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix
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.edgeR.count_matrix
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_GSNO.voom.count_matrix
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.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset
test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset
test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix
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.edgeR.count_matrix
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_37_vs_wt_ph8.voom.count_matrix
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.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset
test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset
test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix
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.edgeR.count_matrix
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/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.count_matrix
test-data/count/express_bowtie/results.xprs
test-data/count/express_bowtie/results_B.xprs
test-data/count/express_bowtie/sample_A
test-data/count/express_bowtie/sample_B
test-data/count/kallisto/abundance.tsv
test-data/count/kallisto/abundance.tsv.genes
test-data/count/kallisto/abundance_B.tsv
test-data/count/kallisto/abundance_B.tsv.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.prcomp.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.isoforms.results
test-data/count/rsem_bowtie/RSEM.isoforms_B.results
test-data/count/rsem_bowtie/sample_A
test-data/count/rsem_bowtie/sample_B
test-data/count/rsem_bowtie2/RSEM.isoforms.results
test-data/count/rsem_bowtie2/RSEM.isoforms_B.results
test-data/count/rsem_bowtie2/sample_A
test-data/count/rsem_bowtie2/sample_B
test-data/count/salmon/sample_A
test-data/count/salmon/sample_B
test-data/count/samples.txt
test-data/count/trinotate/genes.lengths.txt
test-data/count/trinotate/go_annotations.txt
test-data/filtered/Trinity_filtered_exp.fasta
test-data/filtered/Trinity_filtered_hi_iso.fasta
test-data/filtered/Trinity_filtered_pct_iso.fasta
test-data/filtered/counts.matrix
test-data/norm/Trinity.fasta
test-data/norm/Trinity.map
test-data/norm/Trinity_paired_unmerged_1.fasta
test-data/norm/Trinity_paired_unmerged_1.map
test-data/raw/Trinity.fasta
test-data/raw/Trinity.map
test-data/raw/Trinity_single_unmerged_1.fasta
test-data/raw/Trinity_single_unmerged_1.map
test-data/raw/map.tsv
test-data/reads.left.fq
test-data/reads.right.fq
test-data/samples.tsv
test-data/supertranscripts/trinity_genes.fasta
test-data/supertranscripts/trinity_genes.gtf
test-data/supertranscripts/trinity_genes.malign
b
diff -r 000000000000 -r 64094e19077d README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,30 @@
+Trinity memory usage
+====================
+
+As described on the official Trinity website
+`FAQ <http://trinityrnaseq.sourceforge.net/trinity_faq.html#ques_comp_resources_required>`_,
+trinity requires a large amount of memory to perform the assembly: "roughly
+~1G of RAM per 1M reads to be assembled"
+
+By default, this tool is configured to limit the memory consumption to 1G.
+You might need to lower this limit if the machine(s) executing the jobs have less memory available.
+If you have a lot of reads to assemble and a machine with enough memory, you can increase it.
+In both cases, you can set the GALAXY_MEMORY_MB environmental variable in the destination section of the job_conf.xml file::
+
+    <?xml version="1.0"?>
+    <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
+    <job_conf>
+        <plugins>
+            <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
+        </plugins>
+        <handlers>
+            <handler id="main"/>
+        </handlers>
+        <destinations>
+            <destination id="local" runner="local">
+                <env id="GALAXY_MEMORY_MB">1G</env>
+            </destination>
+        </destinations>
+    </job_conf>
+
+
b
diff -r 000000000000 -r 64094e19077d macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,39 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2.6.6">trinity</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+
+    <token name="@WRAPPER_VERSION@">2.6.6</token>
+
+    <token name="@COMMAND_PAIRED_STRAND_JACCARD@">
+        #if $pool.inputs.strand.is_strand_specific:
+            --SS_lib_type $pool.inputs.strand.library_type
+        #end if
+
+        $pool.inputs.jaccard_clip
+    </token>
+
+    <xml name="input_paired_strand_jaccard">
+        <conditional name="strand">
+            <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
+            <when value="false" />
+            <when value="true">
+                <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type">
+                    <option value="FR">Forward-Reverse</option>
+                    <option value="RF">Reverse-Forward</option>
+                </param>
+            </when>
+        </conditional>
+        <param name="jaccard_clip" argument="--jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="Set if you expect high gene density with UTR overlap"/>
+    </xml>
+
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1038/nbt.1883</citation>
+        </citations>
+    </xml>
+</macros>
b
diff -r 000000000000 -r 64094e19077d super_transcripts.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/super_transcripts.xml Thu Jun 14 03:12:34 2018 -0400
[
@@ -0,0 +1,35 @@
+<tool id="trinity_super_transcripts" name="Generate SuperTranscripts" version="@WRAPPER_VERSION@">
+    <description>from a Trinity assembly</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
+       Trinity_gene_splice_modeler.py --incl_malign --trinity_fasta '$assembly'
+    ]]></command>
+    <inputs>
+        <param format="fasta" name="assembly" type="data" label="Trinity assembly"/>
+    </inputs>
+    <outputs>
+        <data format="fasta" name="seqs" from_work_dir="trinity_genes.fasta" label="${tool.name} on ${on_string}: SuperTranscripts sequences"/>
+        <data format="gtf" name="annotation" from_work_dir="trinity_genes.gtf" label="${tool.name} on ${on_string}: SuperTranscripts strcture annotation"/>
+        <data format="clustal" name="malign" from_work_dir="trinity_genes.malign" label="${tool.name} on ${on_string}: multiple alignment of SuperTranscripts"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/>
+            <output name="seqs" file="supertranscripts/trinity_genes.fasta" />
+            <output name="annotation" file="supertranscripts/trinity_genes.gtf" />
+            <output name="malign" file="supertranscripts/trinity_genes.malign" />
+        </test>
+    </tests>
+    <help>
+        SuperTranscripts provide a gene-like view of the transcriptional complexity of a gene. SuperTranscripts were originally defined by Nadia Davidson, Anthony Hawkins, and Alicia Oshlack as described in their publication "SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes" Genome Biology, 2017. SuperTranscripts are useful in the context of genome-free de novo transcriptome assembly in that they provide a genome-like reference for studying aspects of the gene including differential transcript usage (aka. differential exon usage) and as a substrate for mapping reads and identifying allelic polymorphisms.
+
+        A SuperTranscript is constructed by collapsing unique and common sequence regions among splicing isoforms into a single linear sequence.
+
+        .. _Trinity: http://trinityrnaseq.github.io
+    </help>
+
+    <expand macro="citation" />
+</tool>
b
diff -r 000000000000 -r 64094e19077d test-data/count/Trinity.map
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/Trinity.map Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,7 @@
+TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1
+TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1
+TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1
+TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1
+TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1
+TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1
+TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1
b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,1 @@
+category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR under_represented_FDR
b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,1 @@
+category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR
b
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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@@ -0,0 +1,4 @@
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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@@ -0,0 +1,7 @@
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.depleted Thu Jun 14 03:12:34 2018 -0400
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@@ -0,0 +1,1 @@
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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@@ -0,0 +1,2 @@
+category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR go_term
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b
diff -r 000000000000 -r 64094e19077d 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
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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@@ -0,0 +1,1 @@
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diff -r 000000000000 -r 64094e19077d 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
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b
@@ -0,0 +1,3 @@
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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[
@@ -0,0 +1,46 @@
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+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 64094e19077d test-data/count/contig_exn50_statistic/matrix.TMM.EXPR.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/contig_exn50_statistic/matrix.TMM.EXPR.matrix Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,8 @@
+ sample_A sample_B
+TRINITY_DN2_c2_g1_i1 525311.050 145165.140
+TRINITY_DN2_c1_g1_i1 145165.140 525311.050
+TRINITY_DN2_c0_g1_i1 0.000 0.000
+TRINITY_DN1_c0_g1_i1 329523.810 329523.810
+TRINITY_DN3_c0_g1_i1 0.000 0.000
+TRINITY_DN2_c3_g1_i1 0.000 0.000
+TRINITY_DN0_c0_g1_i1 0.000 0.000
b
diff -r 000000000000 -r 64094e19077d test-data/count/define_clusters_by_cutting_tree/my_cluster_plots.pdf
b
Binary file test-data/count/define_clusters_by_cutting_tree/my_cluster_plots.pdf has changed
b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,7 @@
+wt_37_2 wt_37_3 wt_37_1 wt_ph8_3 wt_ph8_1 wt_ph8_2 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2
+TR24|c0_g1_i1 0.106533882165825 -0.313797916782532 0.025003996669227 1.39963914188743 1.22079106142351 1.25695072471892 -1.19180739240392 -1.23133575659056 -1.2719777410879
+TR2779|c0_g1_i1 -0.795433018475884 -1.23380302158535 -0.574143153586594 1.74646076035339 1.75438767612502 1.74380874666379 -1.13287411273457 -0.795433018475884 -0.712970858283911
+TR3091|c0_g1_i1 -2.42438780178849 -2.77802475640319 -2.62602166295814 1.43575453462855 1.4783149968566 1.36038927229391 1.02359379610527 1.32351327005887 1.20686835120661
+TR131|c0_g1_i1 -3.50802026981862 -3.6944333940495 -3.55241438917708 1.98577454287534 1.99158406095747 1.95736061514986 1.41625240401813 1.71671228997234 1.68718414007205
+TR5075|c0_g1_i1 -1.04544737992556 -0.329240345926152 -0.393370683345868 2.50474970263492 2.07793503557972 2.30706903479522 -2.04544737992556 -1.68287730054085 -1.39337068334587
+TR3788|c0_g1_i1 -1.22775484082629 -0.443483531881724 -0.874117886211586 -0.353285722910146 -0.874117886211586 -0.590324920210995 1.12588211378841 1.65760259323259 1.57960008123132
b
diff -r 000000000000 -r 64094e19077d test-data/count/define_clusters_by_cutting_tree/subcluster_2_log2_medianCentered_fpkm.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/define_clusters_by_cutting_tree/subcluster_2_log2_medianCentered_fpkm.matrix Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,8 @@
+wt_37_2 wt_37_3 wt_37_1 wt_ph8_3 wt_ph8_1 wt_ph8_2 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2
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+TR127|c1_g1_i1 1.25755965737847 2.52059406321227 2.02309440374145 -0.0643684375088904 -1.06436843750889 -1.06436843750889 -0.479405936787734 -2.06436843750889 -1.06436843750889
+TR2107|c1_g1_i1 2.49178842221691 2.62929194596684 2.16986032732955 -1.41510217339161 -2.41510217339161 -1.83013967267045 -0.607747251334006 -0.607747251334006 -0.41510217339161
+TR5055|c0_g2_i1 1.90528891290538 0.865760548718745 1.50319046933404 -0.982236357836205 -0.982236357836205 0.280798047997588 -0.982236357836205 -0.304164452723568 -1.30416445272357
+TR4761|c0_g1_i1 2.06406810079911 1.80544476674762 1.90822498634624 -0.339510283104669 -0.357888812419525 -0.296334141902888 -1.67981690730689 -1.51400801433681 -1.59017969482221
+TR1894|c2_g1_i1 2.11263053903627 1.56008951600749 1.23816142112012 -1.34680107960103 -0.346801079601032 -1.34680107960103 -1.34680107960103 -0.761838578879876 0.238161421120124
b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,38 @@
+sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj
+TR4277|c0_g1_i1 wt_37 wt_GSNO 3852.97388871986 161.116814813422 2007.04535176664 4.57661492404411 0.121615845393926 37.6317321909822 0 0
+TR131|c0_g1_i1 wt_37 wt_GSNO 26.1866396538608 1340.30918254958 683.247911101723 -5.68565819121436 0.188173369545147 -30.2149990987446 1.50487696827007e-200 2.48304699764561e-199
+TR4761|c0_g1_i1 wt_37 wt_GSNO 1645.20640957447 193.196157329029 919.201283451752 3.09227622940716 0.143766888218038 21.5089598706302 1.28350063536341e-102 1.41185069889975e-101
+TR3091|c0_g1_i1 wt_37 wt_GSNO 16.7444693227929 328.569936894811 172.657203108802 -4.30529554105297 0.242003292489129 -17.790235400398 8.41257542125902e-71 6.94037472253869e-70
+TR3638|c0_g1_i1 wt_37 wt_GSNO 583.00358519031 183.754416330029 383.37900076017 1.66225356244238 0.144704273829595 11.487245804501 1.5290952692426e-30 1.00920287770012e-29
+TR2487|c0_g1_i1 wt_37 wt_GSNO 342.210853400436 920.407318992504 631.30908619647 -1.42823125318501 0.124766100464837 -11.44727011475 2.42667678803784e-30 1.33467223342081e-29
+TR3788|c0_g1_i1 wt_37 wt_GSNO 19.5075441237117 134.95369713876 77.2306206312357 -2.78185518936858 0.26452057618315 -10.5165928091827 7.24461724546031e-26 3.41531955857415e-25
+TR1479|c0_g1_i1 wt_37 wt_GSNO 129.593534475689 371.064629188207 250.329081831948 -1.51632040995179 0.145721574162902 -10.405599985193 2.33778717307793e-25 9.64337208894648e-25
+TR2107|c1_g1_i1 wt_37 wt_GSNO 48.9228907410258 7.40521775805688 28.1640542495414 2.72565745131165 0.439033221898883 6.20831708252687 5.35550100392654e-10 1.96368370143973e-09
+TR3854|c0_g1_i1 wt_37 wt_GSNO 1573.69549271337 2374.56159860719 1974.12854566028 -0.593952181868433 0.11125243839418 -5.33877900063632 9.35746226940931e-08 3.08796254890507e-07
+TR2122|c0_g2_i2 wt_37 wt_GSNO 119.534640490118 199.143666337033 159.339153413576 -0.73989736621081 0.168946597067547 -4.37947481070002 1.18965671308434e-05 3.56897013925302e-05
+TR1449|c0_g1_i1 wt_37 wt_GSNO 180.814952011467 104.755290736358 142.785121373912 0.785811747593425 0.186397685526418 4.2157806057203 2.48915666101662e-05 6.6882655779165e-05
+TR4163|c0_g1_i1 wt_37 wt_GSNO 347.283468916919 232.772947466212 290.028208191566 0.5773903092812 0.137377906430929 4.20293425836637 2.63477128827014e-05 6.6882655779165e-05
+TR2672|c0_g1_i1 wt_37 wt_GSNO 18.3155337236093 2.26581902751323 10.2906763755613 2.9857084616452 0.761209385049731 3.92232218924907 8.76996107235725e-05 0.000206720510991278
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+TR2844|c0_g1_i1 wt_37 wt_GSNO 158.206282615139 231.762548186068 194.984415400603 -0.551426184671915 0.155135532159318 -3.55448024702441 0.000378726959348647 0.000781124353656584
+TR127|c1_g1_i1 wt_37 wt_GSNO 13.461799216177 1.21881296083961 7.34030608850831 3.52517488060096 1.00261297574214 3.51598769005717 0.00043812129728732 0.000850470753557739
+TR5212|c0_g1_i1 wt_37 wt_GSNO 65.7079302129484 107.875371765755 86.7916509893515 -0.715754705745061 0.210644233010842 -3.39793164766215 0.000678973819799399 0.0012447853362989
+TR1894|c2_g1_i1 wt_37 wt_GSNO 13.3497721959996 2.96749216411516 8.15863218005739 2.116499695166 0.744618031030184 2.84239651333424 0.00447757649596373 0.00777684338772647
+TR24|c0_g1_i1 wt_37 wt_GSNO 69.9065207344592 41.2394742844514 55.5729975094553 0.763675526543044 0.270944643994893 2.81856660933825 0.00482386011442888 0.00795936918880766
+TR4669|c0_g2_i1 wt_37 wt_GSNO 0 167.096667347181 83.5483336735905 -10.0466852501689 3.90738405199054 -2.57120495873725 0.0101345328521317 0.0159256944819212
+TR2779|c0_g1_i1 wt_37 wt_GSNO 155.915506826481 205.619872596257 180.767689711369 -0.403209397282846 0.18950756245476 -2.12766916559914 0.033364523163095 0.0500467847446426
+TR3807|c0_g1_i1 wt_37 wt_GSNO 3.48709246029019 0.350050334268211 1.9185713972792 3.04810928058763 1.5874506366217 1.92012854464212 0.0548416645360559 0.0786858665082542
+TR1492|c0_g1_i2 wt_37 wt_GSNO 1640.89375005483 1435.64893261411 1538.27134133447 0.192601921423703 0.101311986688049 1.90107733270247 0.0572918841322824 0.0787763406818883
+TR4084|c0_g1_i1 wt_37 wt_GSNO 93.2264707954139 121.352438036668 107.289454416041 -0.381231151484282 0.21399248813321 -1.78151651401411 0.0748281095286258 0.0987731045777861
+TR1891|c0_g1_i1 wt_37 wt_GSNO 107.628573623499 135.399287466928 121.513930545214 -0.329513668205708 0.189733845104182 -1.7367152814764 0.0824374390602291 0.104632134191829
+TR1837|c2_g1_i1 wt_37 wt_GSNO 0.308903905435236 2.22601224010275 1.26745807276899 -2.87715913917267 1.7927876855897 -1.60485213184979 0.108526350064413 1
+TR5075|c0_g1_i1 wt_37 wt_GSNO 15.8633018853512 9.23822794034992 12.5507649128506 0.776103293030194 0.516446682273215 1.5027752518693 0.13289700980576 0.16070937436521
+TR4859|c0_g1_i1 wt_37 wt_GSNO 7.32690480813971 3.17910584569163 5.25300532691567 1.23041974278822 0.82607009598701 1.48948587869905 0.13635946915836 0.16070937436521
+TR939|c0_g1_i1 wt_37 wt_GSNO 84.2568220960088 96.9171174594069 90.5869697777078 -0.203187486812458 0.203052234052517 -1.00066609835923 0.316988262617008 0.354139456794138
+TR2278|c0_g1_i1 wt_37 wt_GSNO 486.5272515724 448.140178813055 467.333715192727 0.118924512672215 0.120068895863502 0.990468945491189 0.321944960721944 0.354139456794138
+TR2011|c5_g1_i1 wt_37 wt_GSNO 5.60408627995835 7.88255079488408 6.74331853742122 -0.50342873702063 0.712267625142964 -0.706797163383052 0.479692537619295 0.510640443272153
+TR2182|c3_g2_i6 wt_37 wt_GSNO 2.24974854180929 1.3031439398571 1.77644624083319 0.878491642458712 1.45214866443311 0.604959852923637 0.545205672528741 0.562243349795264
+TR3249|c0_g1_i1 wt_37 wt_GSNO 1.12573841927462 2.128954842887 1.62734663108081 -0.858277190977929 1.45820967054459 -0.588582841216099 0.556141147160533 1
+TR1678|c0_g1_i1 wt_37 wt_GSNO 0.595141051681226 0.700100668536423 0.647620860108824 -0.322353878735801 2.26929239960538 -0.142050393678601 0.887040200834538 1
+TR1122|c0_g1_i1 wt_37 wt_GSNO 1.41370386226057 1.3031439398571 1.35842390105883 0.189589394350501 1.67633508161709 0.113097552171736 0.909953215626095 1
+TR1982|c2_g1_i1 wt_37 wt_GSNO 5.73684100209948 5.71221669652109 5.72452884931028 -0.0104554076697487 0.738553450989727 -0.0141566025529196 0.988705042660126 0.988705042660126
b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf
b
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf has changed
b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/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/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,7 @@
+sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2
+TR4277|c0_g1_i1 wt_37 wt_GSNO 3852.97388871986 161.116814813422 2007.04535176664 4.57260002898197 0.121471586836965 37.6433711623376 0 0 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00
+TR4761|c0_g1_i1 wt_37 wt_GSNO 1645.20640957447 193.196157329029 919.201283451752 3.08848040390227 0.143569117275296 21.5121501233448 1.19819880470067e-102 1.47777852579749e-101 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00
+TR2107|c1_g1_i1 wt_37 wt_GSNO 48.9228907410258 7.40521775805688 28.1640542495414 2.69488884014666 0.432209832999676 6.23514005094067 4.51374085119887e-10 1.85564901660398e-09 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00
+TR2672|c0_g1_i1 wt_37 wt_GSNO 18.3155337236093 2.26581902751323 10.2906763755613 2.88788179640237 0.725539563189254 3.98032298019437 6.88216980025882e-05 0.000181885916149697 14.00 29.00 22.00 0.00 4.00 2.00 14.00 4.00 7.00
+TR127|c1_g1_i1 wt_37 wt_GSNO 13.461799216177 1.21881296083961 7.34030608850831 3.33150202228086 0.915899815581865 3.63740877070095 0.000275394687501815 0.000667511143840185 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00
+TR5055|c0_g2_i1 wt_37 wt_GSNO 23.3590211688541 5.52768338415684 14.4433522765055 2.04460941512382 0.563987307210913 3.62527558507482 0.000288653467606567 0.000667511143840185 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00
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diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/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/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,4 @@
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+TR131|c0_g1_i1 wt_37 wt_GSNO 26.1866396538608 1340.30918254958 683.247911101723 -5.67373033438939 0.187375754459626 -30.2799599166492 2.10486694333775e-201 3.89400384517483e-200 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00
+TR3091|c0_g1_i1 wt_37 wt_GSNO 16.7444693227929 328.569936894811 172.657203108802 -4.29037251456992 0.240582794801874 -17.8332474610379 3.90090325510546e-71 3.60833551097255e-70 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00
+TR3788|c0_g1_i1 wt_37 wt_GSNO 19.5075441237117 134.95369713876 77.2306206312357 -2.77036684869735 0.263152237265066 -10.527620351967 6.4442989603998e-26 3.40627230763989e-25 17.00 30.00 22.00 91.00 132.00 125.00 32.00 22.00 27.00
b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,38 @@
+wt_37_1 wt_37_2 wt_37_3 wt_GSNO_1 wt_GSNO_2 wt_GSNO_3
+TR24|c0_g1_i1 85 90 67 35 34 36
+TR2779|c0_g1_i1 217 186 137 186 197 147
+TR127|c1_g1_i1 16 9 23 0 1 2
+TR2107|c1_g1_i1 47 59 65 6 7 6
+TR2011|c5_g1_i1 4 11 4 5 7 8
+TR4163|c0_g1_i1 425 368 422 216 210 172
+TR5055|c0_g2_i1 27 36 17 7 3 4
+TR1449|c0_g1_i1 207 196 230 113 91 66
+TR1982|c2_g1_i1 6 7 7 3 8 4
+TR1492|c0_g1_i2 1921 1895 1906 1263 1319 1104
+TR1122|c0_g1_i1 0 2 3 0 0 3
+TR2278|c0_g1_i1 598 497 610 406 413 333
+TR4084|c0_g1_i1 86 95 148 111 127 77
+TR4761|c0_g1_i1 1875 2089 1746 174 165 155
+TR3638|c0_g1_i1 712 647 676 184 174 117
+TR3854|c0_g1_i1 1864 1878 1734 2173 2151 1775
+TR131|c0_g1_i1 31 32 28 1233 1208 1001
+TR5075|c0_g1_i1 21 13 22 8 10 6
+TR2182|c3_g2_i6 4 1 3 0 0 3
+TR3788|c0_g1_i1 22 17 30 132 125 91
+TR4859|c0_g1_i1 8 6 12 1 3 4
+TR2487|c0_g1_i1 424 386 383 866 806 689
+TR2122|c0_g2_i2 136 145 135 157 201 155
+TR4277|c0_g1_i1 4284 4466 4701 134 164 118
+TR4669|c0_g2_i1 0 0 0 0 218 209
+TR3091|c0_g1_i1 19 22 17 308 284 250
+TR3807|c0_g1_i1 2 6 4 0 1 0
+TR1894|c2_g1_i1 11 21 14 2 5 1
+TR5212|c0_g1_i1 78 64 89 98 108 73
+TR939|c0_g1_i1 99 96 99 89 88 72
+TR1891|c0_g1_i1 124 115 138 139 111 97
+TR2672|c0_g1_i1 22 14 29 4 2 0
+TR2844|c0_g1_i1 178 166 211 214 223 161
+TR1837|c2_g1_i1 0 1 0 1 4 1
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+TR1479|c0_g1_i1 141 136 178 324 354 277
b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,38 @@
+sampleA sampleB logFC logCPM PValue FDR
+TR131|c0_g1_i1 wt_37 wt_GSNO -5.83641794955382 16.0393491449056 0 0
+TR4277|c0_g1_i1 wt_37 wt_GSNO 4.41329536892161 17.453649857324 0 0
+TR3091|c0_g1_i1 wt_37 wt_GSNO -4.45192710783926 14.0403115023365 4.66239713643175e-192 5.75028980159916e-191
+TR4761|c0_g1_i1 wt_37 wt_GSNO 2.92754337500687 16.3361488759619 3.05265683396309e-191 2.82370757141586e-190
+TR2487|c0_g1_i1 wt_37 wt_GSNO -1.58705168340508 15.8893887856701 9.57106937146597e-124 7.08259133488482e-123
+TR1479|c0_g1_i1 wt_37 wt_GSNO -1.67065982572176 14.5610246448295 4.39649357092684e-84 2.71117103540489e-83
+TR3638|c0_g1_i1 wt_37 wt_GSNO 1.49937182627392 15.1071990563814 1.60652562072048e-64 8.49163542380826e-64
+TR3854|c0_g1_i1 wt_37 wt_GSNO -0.756864683109858 17.5153338325952 9.14141417630157e-40 4.22790405653948e-39
+TR2122|c0_g2_i2 wt_37 wt_GSNO -0.90394318029981 13.8984589155106 3.98287653266084e-13 1.63740479676057e-12
+TR2844|c0_g1_i1 wt_37 wt_GSNO -0.707834005847516 14.1849675326065 1.90004997002049e-12 7.0301848890758e-12
+TR3788|c0_g1_i1 wt_37 wt_GSNO -2.92402824575823 12.8707284018497 1.35908019280542e-09 4.57145155761824e-09
+TR4669|c0_g2_i1 wt_37 wt_GSNO -10.5373989771184 13.0207784411552 2.87822490296537e-08 8.87452678414323e-08
+TR2672|c0_g1_i1 wt_37 wt_GSNO 2.77705541360002 10.2430402179839 7.41806563943484e-08 2.11129560506992e-07
+TR4163|c0_g1_i1 wt_37 wt_GSNO 0.420123134789911 14.7306522277754 2.74345107938324e-06 7.25054928122714e-06
+TR127|c1_g1_i1 wt_37 wt_GSNO 3.26487561187968 9.85808314705506 6.1191913603037e-06 1.50940053554158e-05
+TR2107|c1_g1_i1 wt_37 wt_GSNO 2.54741701164587 11.489948731934 1.24782096095324e-05 2.88558597220436e-05
+TR2779|c0_g1_i1 wt_37 wt_GSNO -0.571512278204146 14.0677635717422 7.39487278515011e-05 0.000160947231206208
+TR1894|c2_g1_i1 wt_37 wt_GSNO 1.88989717290856 9.93884262525918 0.00064827406279645 0.00133256335130381
+TR5055|c0_g2_i1 wt_37 wt_GSNO 1.89504810994952 10.6064804346292 0.00584438080176016 0.011381162613954
+TR3807|c0_g1_i1 wt_37 wt_GSNO 2.66606066906632 8.56455983886691 0.0188051214716541 0.0347894747225602
+TR5212|c0_g1_i1 wt_37 wt_GSNO -0.867441722907523 13.0312878134755 0.0313380642877521 0.055214684697468
+TR1449|c0_g1_i1 wt_37 wt_GSNO 0.636828244112651 13.716963541734 0.0836258106887223 0.140643408885578
+TR1837|c2_g1_i1 wt_37 wt_GSNO -2.70136949048315 8.19724487849862 0.11443273811818 0.184087448277072
+TR4859|c0_g1_i1 wt_37 wt_GSNO 1.06021338602227 9.44252758756623 0.17021260004507 0.262411091736149
+TR4084|c0_g1_i1 wt_37 wt_GSNO -0.527027354857722 13.3333941866224 0.195100037539558 0.280916147575458
+TR1891|c0_g1_i1 wt_37 wt_GSNO -0.481344817930584 13.5015018099629 0.197400536134106 0.280916147575458
+TR24|c0_g1_i1 wt_37 wt_GSNO 0.590686928315332 12.3882336221811 0.209814398393357 0.287523434835341
+TR2011|c5_g1_i1 wt_37 wt_GSNO -0.668008806764204 9.63014074618193 0.239244885423374 0.316145027166602
+TR939|c0_g1_i1 wt_37 wt_GSNO -0.361607139894815 13.0833886152319 0.340252678428006 0.434115486270215
+TR5075|c0_g1_i1 wt_37 wt_GSNO 0.617585416067661 10.4358029661318 0.377913209145196 0.466092957945741
+TR1492|c0_g1_i2 wt_37 wt_GSNO 0.0311900896664335 17.1368189470585 0.559289231968699 0.657620159615942
+TR3249|c0_g1_i1 wt_37 wt_GSNO -0.894241538356016 8.33957569586088 0.568752570478653 0.657620159615942
+TR2278|c0_g1_i1 wt_37 wt_GSNO -0.0373200220187202 15.4258149088647 0.636489077475997 0.713639268685208
+TR2182|c3_g2_i6 wt_37 wt_GSNO 0.714549920613349 8.45775163335771 0.790296098133788 0.860028106792652
+TR1982|c2_g1_i1 wt_37 wt_GSNO -0.181275971858276 9.49467590956657 0.873422282667325 0.923332127391172
+TR1678|c0_g1_i1 wt_37 wt_GSNO -0.476606391142577 7.93769527756871 1 1
+TR1122|c0_g1_i1 wt_37 wt_GSNO 0.0647357997613641 8.26206759454538 1 1
b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf
b
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf has changed
b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.count_matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.count_matrix Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,38 @@
+wt_37_1 wt_37_2 wt_37_3 wt_GSNO_1 wt_GSNO_2 wt_GSNO_3
+TR24|c0_g1_i1 85 90 67 35 34 36
+TR2779|c0_g1_i1 217 186 137 186 197 147
+TR127|c1_g1_i1 16 9 23 0 1 2
+TR2107|c1_g1_i1 47 59 65 6 7 6
+TR2011|c5_g1_i1 4 11 4 5 7 8
+TR4163|c0_g1_i1 425 368 422 216 210 172
+TR5055|c0_g2_i1 27 36 17 7 3 4
+TR1449|c0_g1_i1 207 196 230 113 91 66
+TR1982|c2_g1_i1 6 7 7 3 8 4
+TR1492|c0_g1_i2 1921 1895 1906 1263 1319 1104
+TR1122|c0_g1_i1 0 2 3 0 0 3
+TR2278|c0_g1_i1 598 497 610 406 413 333
+TR4084|c0_g1_i1 86 95 148 111 127 77
+TR4761|c0_g1_i1 1875 2089 1746 174 165 155
+TR3638|c0_g1_i1 712 647 676 184 174 117
+TR3854|c0_g1_i1 1864 1878 1734 2173 2151 1775
+TR131|c0_g1_i1 31 32 28 1233 1208 1001
+TR5075|c0_g1_i1 21 13 22 8 10 6
+TR2182|c3_g2_i6 4 1 3 0 0 3
+TR3788|c0_g1_i1 22 17 30 132 125 91
+TR4859|c0_g1_i1 8 6 12 1 3 4
+TR2487|c0_g1_i1 424 386 383 866 806 689
+TR2122|c0_g2_i2 136 145 135 157 201 155
+TR4277|c0_g1_i1 4284 4466 4701 134 164 118
+TR4669|c0_g2_i1 0 0 0 0 218 209
+TR3091|c0_g1_i1 19 22 17 308 284 250
+TR3807|c0_g1_i1 2 6 4 0 1 0
+TR1894|c2_g1_i1 11 21 14 2 5 1
+TR5212|c0_g1_i1 78 64 89 98 108 73
+TR939|c0_g1_i1 99 96 99 89 88 72
+TR1891|c0_g1_i1 124 115 138 139 111 97
+TR2672|c0_g1_i1 22 14 29 4 2 0
+TR2844|c0_g1_i1 178 166 211 214 223 161
+TR1837|c2_g1_i1 0 1 0 1 4 1
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+TR1479|c0_g1_i1 141 136 178 324 354 277
b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,38 @@
+sampleA sampleB logFC logCPM PValue FDR
+TR131|c0_g1_i1 wt_37 wt_GSNO -5.82360148900389 16.1142242655408 6.54502972918692e-10 2.42166099979916e-08
+TR4277|c0_g1_i1 wt_37 wt_GSNO 4.41183386172098 17.3836256000268 1.7102544921365e-09 3.16397081045253e-08
+TR3091|c0_g1_i1 wt_37 wt_GSNO -4.43700179801176 14.1203688767724 4.42033048679943e-08 5.45174093371929e-07
+TR2487|c0_g1_i1 wt_37 wt_GSNO -1.58598083708684 15.9280757073272 7.01720228399608e-08 6.49091211269637e-07
+TR4761|c0_g1_i1 wt_37 wt_GSNO 2.92043321768346 16.2716301848411 5.72725934421127e-07 4.23817191471634e-06
+TR1479|c0_g1_i1 wt_37 wt_GSNO -1.67738254434993 14.6016057367881 1.03919750932427e-06 5.8615543150164e-06
+TR3638|c0_g1_i1 wt_37 wt_GSNO 1.50288215872986 15.0600281889274 1.12469315856867e-06 5.8615543150164e-06
+TR3788|c0_g1_i1 wt_37 wt_GSNO -2.93907650045598 12.9393872783943 2.35975448958169e-06 9.70121290161359e-06
+TR3854|c0_g1_i1 wt_37 wt_GSNO -0.759397690410038 17.5353083640786 1.26736309513868e-06 5.8615543150164e-06
+TR2107|c1_g1_i1 wt_37 wt_GSNO 2.46233758474327 11.260249244859 0.000163907571391062 0.000551325467406299
+TR2122|c0_g2_i2 wt_37 wt_GSNO -0.898543060702643 13.9151768182402 0.000124408949544541 0.000460313113314803
+TR2844|c0_g1_i1 wt_37 wt_GSNO -0.712202725875737 14.1973066750225 0.000243984033514546 0.000752284103336518
+TR5212|c0_g1_i1 wt_37 wt_GSNO -0.87701850957337 13.0391017777502 0.000473838954429694 0.00134861856260759
+TR4163|c0_g1_i1 wt_37 wt_GSNO 0.417694804483349 14.7107025605232 0.000805848497363634 0.00212974245731817
+TR2672|c0_g1_i1 wt_37 wt_GSNO 2.90562993555483 9.81450205355949 0.00822748279906008 0.0169120479758457
+TR1449|c0_g1_i1 wt_37 wt_GSNO 0.640011354440497 13.6755402195434 0.00227354555819909 0.00560807904355776
+TR127|c1_g1_i1 wt_37 wt_GSNO 3.09466453837236 9.33233275488244 0.00997545255499303 0.0184545872267371
+TR1894|c2_g1_i1 wt_37 wt_GSNO 1.8273232048322 9.47625819175118 0.0170307015491222 0.0286425435144327
+TR5055|c0_g2_i1 wt_37 wt_GSNO 1.79897959483123 10.2910629958573 0.0144290410083875 0.025422596062397
+TR939|c0_g1_i1 wt_37 wt_GSNO -0.363394684962815 13.0708604932728 0.00579686595094712 0.0134052525115652
+TR1837|c2_g1_i1 wt_37 wt_GSNO -2.21418127698954 7.02378849272624 0.0306005987832276 0.0471759231241425
+TR1891|c0_g1_i1 wt_37 wt_GSNO -0.477062796219233 13.500309435849 0.00675073796972544 0.0146927826399907
+TR3807|c0_g1_i1 wt_37 wt_GSNO 1.91879773659378 7.35599058475032 0.0402625583382777 0.0572967176352414
+TR2779|c0_g1_i1 wt_37 wt_GSNO -0.600036558858359 14.0748557225205 0.00991998269314111 0.0184545872267371
+TR24|c0_g1_i1 wt_37 wt_GSNO 0.588796779058576 12.310400953631 0.0185008090691583 0.0297621711112546
+TR4859|c0_g1_i1 wt_37 wt_GSNO 1.06036244689068 8.9138577436531 0.104550838513832 0.143273371296733
+TR4084|c0_g1_i1 wt_37 wt_GSNO -0.567278869966665 13.330468891507 0.0372234219214301 0.0550906644437166
+TR2011|c5_g1_i1 wt_37 wt_GSNO -0.789577978066661 9.33004998835934 0.161975973261362 0.206659000367944
+TR2182|c3_g2_i6 wt_37 wt_GSNO 1.02218394394404 7.37517597546907 0.329234058043314 0.406055338253421
+TR5075|c0_g1_i1 wt_37 wt_GSNO 0.549449880041588 10.1791103984097 0.127566698813275 0.168570280574684
+TR4669|c0_g2_i1 wt_37 wt_GSNO -6.27345157840298 13.126293325041 0.423017017822531 0.489113426857301
+TR1678|c0_g1_i1 wt_37 wt_GSNO -0.330222398445961 5.95523974949609 0.735881722270124 0.79829094077818
+TR1122|c0_g1_i1 wt_37 wt_GSNO 0.193564460109425 7.01613737702005 0.875819231521416 0.875819231521416
+TR3249|c0_g1_i1 wt_37 wt_GSNO -0.276543877903423 7.32180296800742 0.776715509946338 0.79829094077818
+TR1982|c2_g1_i1 wt_37 wt_GSNO -0.131251756802268 9.08566155151058 0.763275890632561 0.79829094077818
+TR2278|c0_g1_i1 wt_37 wt_GSNO -0.0407242590322052 15.424279874284 0.616230913043451 0.69092556916993
+TR1492|c0_g1_i2 wt_37 wt_GSNO 0.0323916193661019 17.1363857315734 0.39613877470297 0.472810795613223
b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf
b
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf has changed
b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.count_matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.count_matrix Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,38 @@
+wt_37_1 wt_37_2 wt_37_3 wt_GSNO_1 wt_GSNO_2 wt_GSNO_3
+TR24|c0_g1_i1 85 90 67 35 34 36
+TR2779|c0_g1_i1 217 186 137 186 197 147
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+TR4163|c0_g1_i1 425 368 422 216 210 172
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+TR1449|c0_g1_i1 207 196 230 113 91 66
+TR1982|c2_g1_i1 6 7 7 3 8 4
+TR1492|c0_g1_i2 1921 1895 1906 1263 1319 1104
+TR1122|c0_g1_i1 0 2 3 0 0 3
+TR2278|c0_g1_i1 598 497 610 406 413 333
+TR4084|c0_g1_i1 86 95 148 111 127 77
+TR4761|c0_g1_i1 1875 2089 1746 174 165 155
+TR3638|c0_g1_i1 712 647 676 184 174 117
+TR3854|c0_g1_i1 1864 1878 1734 2173 2151 1775
+TR131|c0_g1_i1 31 32 28 1233 1208 1001
+TR5075|c0_g1_i1 21 13 22 8 10 6
+TR2182|c3_g2_i6 4 1 3 0 0 3
+TR3788|c0_g1_i1 22 17 30 132 125 91
+TR4859|c0_g1_i1 8 6 12 1 3 4
+TR2487|c0_g1_i1 424 386 383 866 806 689
+TR2122|c0_g2_i2 136 145 135 157 201 155
+TR4277|c0_g1_i1 4284 4466 4701 134 164 118
+TR4669|c0_g2_i1 0 0 0 0 218 209
+TR3091|c0_g1_i1 19 22 17 308 284 250
+TR3807|c0_g1_i1 2 6 4 0 1 0
+TR1894|c2_g1_i1 11 21 14 2 5 1
+TR5212|c0_g1_i1 78 64 89 98 108 73
+TR939|c0_g1_i1 99 96 99 89 88 72
+TR1891|c0_g1_i1 124 115 138 139 111 97
+TR2672|c0_g1_i1 22 14 29 4 2 0
+TR2844|c0_g1_i1 178 166 211 214 223 161
+TR1837|c2_g1_i1 0 1 0 1 4 1
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+TR1479|c0_g1_i1 141 136 178 324 354 277
b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,39 @@
+sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj
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+TR5212|c0_g1_i1 wt_37 wt_ph8 80.2050001877881 94.8352723753388 87.5201362815635 -0.236625075567938 0.21614403033503 -1.09475646956875 0.273623341840838 0.335409257740381
+TR3854|c0_g1_i1 wt_37 wt_ph8 1925.26464813324 2107.16376011081 2016.21420412203 -0.130625245556183 0.13088163358419 -0.998041069468758 0.318259444082768 0.377933089848287
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+TR2011|c5_g1_i1 wt_37 wt_ph8 6.84875389533898 4.81927837273561 5.8340161340373 0.48395696149425 0.739237535887472 0.654670438120067 0.512679962329315 0.556623959100399
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b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf
b
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/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/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,7 @@
+sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2
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+TR4761|c0_g1_i1 wt_37 wt_ph8 2012.6141923276 384.620292965437 1198.61724264652 2.38432084623308 0.148099583891604 16.0994432501458 2.57410332221217e-58 2.44539815610156e-57 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00
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b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/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/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,5 @@
+sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2
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+TR2779|c0_g1_i1 wt_37 wt_ph8 191.51955185349 1058.15934185376 624.839446853626 -2.45909834872711 0.247058756007882 -9.95349603658112 2.43476309780354e-23 1.54201662860891e-22 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00
b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,39 @@
+wt_37_1 wt_37_2 wt_37_3 wt_ph8_1 wt_ph8_2 wt_ph8_3
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b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,39 @@
+sampleA sampleB logFC logCPM PValue FDR
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b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf
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diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.count_matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.count_matrix Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,39 @@
+wt_37_1 wt_37_2 wt_37_3 wt_ph8_1 wt_ph8_2 wt_ph8_3
+TR24|c0_g1_i1 85 90 67 196 201 222
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+TR1449|c0_g1_i1 207 196 230 130 107 124
+TR1982|c2_g1_i1 6 7 7 9 11 16
+TR1859|c3_g1_i1 1 0 0 2 4 1
+TR1492|c0_g1_i2 1921 1895 1906 929 922 899
+TR1122|c0_g1_i1 0 2 3 1 0 1
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diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,39 @@
+sampleA sampleB logFC logCPM PValue FDR
+TR131|c0_g1_i1 wt_37 wt_ph8 -5.89108692370307 16.0946870940125 5.83734002581789e-38 2.2181892098108e-36
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b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf
b
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diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.count_matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.count_matrix Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,39 @@
+wt_37_1 wt_37_2 wt_37_3 wt_ph8_1 wt_ph8_2 wt_ph8_3
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b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,40 @@
+sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj
+TR2779|c0_g1_i1 wt_GSNO wt_ph8 195.849684476753 966.924129135581 581.386906806167 -2.30255444666643 0.142496869452374 -16.1586318037394 9.87286349195067e-59 3.65295949202175e-57
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+TR3638|c0_g1_i1 wt_GSNO wt_ph8 174.266398355818 297.555274221606 235.910836288712 -0.761689698593786 0.0969314803260852 -7.85802193499368 3.90246977317854e-15 2.88782763215212e-14
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+TR4277|c0_g1_i1 wt_GSNO wt_ph8 153.969096204861 149.159426886469 151.564261545665 0.0465928591854992 0.127909639606222 0.364263861026723 0.715660983486377 0.882648546299865
+TR3854|c0_g1_i1 wt_GSNO wt_ph8 2260.55060252051 1927.46472630351 2094.00766441201 0.229965172704227 0.793466242289153 0.289823511635197 0.771951259799022 0.910963182508483
+TR127|c1_g1_i1 wt_GSNO wt_ph8 1.20754470361908 1.49113571265046 1.34934020813477 -0.373671738849606 1.38864714646401 -0.269090488394483 0.787860049737066 0.910963182508483
+TR2090|c0_g1_i1 wt_GSNO wt_ph8 9.46045896251181 5.6546754787973 7.55756722065455 0.740040477295998 3.75055668025179 0.197314836272869 0.843581169905129 0.945833432923932
+TR3807|c0_g1_i1 wt_GSNO wt_ph8 0.347502979754365 0.292870809896544 0.320186894825454 0.331202385322154 1.89086385045429 0.175159298350635 0.86095446505486 1
+TR131|c0_g1_i1 wt_GSNO wt_ph8 1275.67603302799 1312.2934796972 1293.9847563626 -0.0408368749216097 0.405274721880973 -0.100763439506112 0.919738250126613 0.956831887096638
+TR5055|c0_g2_i1 wt_GSNO wt_ph8 5.17791343714095 5.60171771495863 5.38981557604979 -0.113901914254779 1.2463123048955 -0.0913911495596841 0.927181793948424 0.956831887096638
+TR939|c0_g1_i1 wt_GSNO wt_ph8 92.2508462008296 94.0990807885678 93.1749634946987 -0.0286723936076206 0.345661698999542 -0.0829492931690373 0.933891858779013 0.956831887096638
+TR2487|c0_g1_i1 wt_GSNO wt_ph8 875.181494043204 882.631049341941 878.906271692572 -0.0122873741271452 0.226999049805604 -0.0541296280212089 0.956831887096638 0.956831887096638
b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf
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Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/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/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,1 @@
+sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2
b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/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/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,3 @@
+sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2
+TR2779|c0_g1_i1 wt_GSNO wt_ph8 195.849684476753 966.924129135581 581.386906806167 -2.26327524632747 0.139880929176731 -16.1800129556472 6.97797522934818e-59 2.3027318256849e-57 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00
+TR24|c0_g1_i1 wt_GSNO wt_ph8 39.3724575919554 183.288101009647 111.330279300801 -2.12198385961523 0.229366226812664 -9.25150964508988 2.21344016014191e-20 1.82608813211707e-19 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00
b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,40 @@
+wt_GSNO_1 wt_GSNO_2 wt_GSNO_3 wt_ph8_1 wt_ph8_2 wt_ph8_3
+TR24|c0_g1_i1 35 34 36 196 201 222
+TR2779|c0_g1_i1 186 197 147 1094 1086 1088
+TR127|c1_g1_i1 0 1 2 1 1 3
+TR2107|c1_g1_i1 6 7 6 1 2 3
+TR2011|c5_g1_i1 5 7 8 4 8 3
+TR4163|c0_g1_i1 216 210 172 254 212 234
+TR5055|c0_g2_i1 7 3 4 4 11 4
+TR1449|c0_g1_i1 113 91 66 130 107 124
+TR1982|c2_g1_i1 3 8 4 9 11 16
+TR1859|c3_g1_i1 0 0 0 2 4 1
+TR1492|c0_g1_i2 1263 1319 1104 929 922 899
+TR1122|c0_g1_i1 0 0 3 1 0 1
+TR2278|c0_g1_i1 406 413 333 409 337 323
+TR4084|c0_g1_i1 111 127 77 201 158 175
+TR4761|c0_g1_i1 174 165 155 389 406 394
+TR3638|c0_g1_i1 184 174 117 344 338 324
+TR2090|c0_g1_i1 0 0 22 0 9 10
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+TR131|c0_g1_i1 1233 1208 1001 1492 1457 1486
+TR5075|c0_g1_i1 8 10 6 121 142 163
+TR2182|c3_g2_i6 0 0 3 2 3 1
+TR3788|c0_g1_i1 132 125 91 22 27 32
+TR4859|c0_g1_i1 1 3 4 1 2 1
+TR2487|c0_g1_i1 866 806 689 989 1032 963
+TR2122|c0_g2_i2 157 201 155 398 344 369
+TR4277|c0_g1_i1 134 164 118 162 170 172
+TR4669|c0_g2_i1 0 218 209 0 0 0
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+TR5212|c0_g1_i1 98 108 73 105 84 103
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b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,40 @@
+sampleA sampleB logFC logCPM PValue FDR
+TR2779|c0_g1_i1 wt_GSNO wt_ph8 -2.23948335958727 15.9163308249372 1.20766376889896e-237 4.70988869870595e-236
+TR1492|c0_g1_i2 wt_GSNO wt_ph8 0.807859120941235 16.8439348559211 2.37986391219743e-61 4.64073462878498e-60
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+TR2278|c0_g1_i1 wt_GSNO wt_ph8 0.490901034745758 15.2921454021456 1.53296499052609e-09 7.47320432881468e-09
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+TR4669|c0_g2_i1 wt_GSNO wt_ph8 10.4044948993067 13.1110475123695 1.35189372056785e-06 4.79307773655872e-06
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+TR1678|c0_g1_i1 wt_GSNO wt_ph8 -3.02812287247775 9.36059212330112 0.0074853976481696 0.0208521791627582
+TR2107|c1_g1_i1 wt_GSNO wt_ph8 1.98032359155541 9.36544178725855 0.0305238827180189 0.0756824353198294
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+TR1859|c3_g1_i1 wt_GSNO wt_ph8 -4.12978123132011 8.37588761488442 0.0428877609330621 0.0983895691993777
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+TR4859|c0_g1_i1 wt_GSNO wt_ph8 1.3062724221166 8.73091245897321 0.181160758857669 0.3364414093071
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+TR1982|c2_g1_i1 wt_GSNO wt_ph8 -0.866592651710305 10.0958159836705 0.312186869456376 0.515984430920105
+TR1894|c2_g1_i1 wt_GSNO wt_ph8 0.989932992780787 8.78384403630691 0.317528880566218 0.515984430920105
+TR4277|c0_g1_i1 wt_GSNO wt_ph8 0.107189584823599 14.0046148411409 0.347278576725125 0.541754579691195
+TR2487|c0_g1_i1 wt_GSNO wt_ph8 0.0467513454249246 16.526653433485 0.376403968202147 0.560230359736405
+TR3249|c0_g1_i1 wt_GSNO wt_ph8 -1.00369455926223 9.08504250192555 0.387851787509819 0.560230359736405
+TR5212|c0_g1_i1 wt_GSNO wt_ph8 0.310409394484433 13.3365591825697 0.416163942507532 0.572783249883747
+TR2011|c5_g1_i1 wt_GSNO wt_ph8 0.799376994792807 9.70509536731836 0.425915749913555 0.572783249883747
+TR1837|c2_g1_i1 wt_GSNO wt_ph8 0.59484087321072 8.66193471010726 0.588495494688377 0.76504414309489
+TR2090|c0_g1_i1 wt_GSNO wt_ph8 0.766971023107968 9.89421471118339 0.638322407555079 0.8030507707951
+TR131|c0_g1_i1 wt_GSNO wt_ph8 0.0187996511046741 17.0827735361623 0.697507705031756 0.850087515507453
+TR1122|c0_g1_i1 wt_GSNO wt_ph8 0.908051089281089 8.22928258978683 0.753364106379395 0.890339398448377
+TR1449|c0_g1_i1 wt_GSNO wt_ph8 -0.0452741219590205 13.4583026590017 0.919111339143084 1
+TR939|c0_g1_i1 wt_GSNO wt_ph8 0.0309689709592036 13.3146949564453 0.956245904999637 1
+TR5055|c0_g2_i1 wt_GSNO wt_ph8 -0.0548476287872344 9.62768102188797 0.999999999999985 1
+TR2182|c3_g2_i6 wt_GSNO wt_ph8 -0.517423422896207 8.5297276065799 1 1
+TR127|c1_g1_i1 wt_GSNO wt_ph8 -0.299043611515333 8.4576897025083 1 1
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diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf
b
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed
b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.count_matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.count_matrix Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,40 @@
+wt_GSNO_1 wt_GSNO_2 wt_GSNO_3 wt_ph8_1 wt_ph8_2 wt_ph8_3
+TR24|c0_g1_i1 35 34 36 196 201 222
+TR2779|c0_g1_i1 186 197 147 1094 1086 1088
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+TR4163|c0_g1_i1 216 210 172 254 212 234
+TR5055|c0_g2_i1 7 3 4 4 11 4
+TR1449|c0_g1_i1 113 91 66 130 107 124
+TR1982|c2_g1_i1 3 8 4 9 11 16
+TR1859|c3_g1_i1 0 0 0 2 4 1
+TR1492|c0_g1_i2 1263 1319 1104 929 922 899
+TR1122|c0_g1_i1 0 0 3 1 0 1
+TR2278|c0_g1_i1 406 413 333 409 337 323
+TR4084|c0_g1_i1 111 127 77 201 158 175
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+TR2090|c0_g1_i1 0 0 22 0 9 10
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+TR131|c0_g1_i1 1233 1208 1001 1492 1457 1486
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+TR2182|c3_g2_i6 0 0 3 2 3 1
+TR3788|c0_g1_i1 132 125 91 22 27 32
+TR4859|c0_g1_i1 1 3 4 1 2 1
+TR2487|c0_g1_i1 866 806 689 989 1032 963
+TR2122|c0_g2_i2 157 201 155 398 344 369
+TR4277|c0_g1_i1 134 164 118 162 170 172
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+TR3807|c0_g1_i1 0 1 0 1 0 0
+TR1894|c2_g1_i1 2 5 1 3 1 1
+TR5212|c0_g1_i1 98 108 73 105 84 103
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diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,40 @@
+sampleA sampleB logFC logCPM PValue FDR
+TR2779|c0_g1_i1 wt_GSNO wt_ph8 -2.23795519272237 15.9076254017254 2.92187316761645e-09 1.13953053537042e-07
+TR1492|c0_g1_i2 wt_GSNO wt_ph8 0.807554446371668 16.8426446227048 5.58321346448906e-08 1.08872662557537e-06
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b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf
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Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed
b
diff -r 000000000000 -r 64094e19077d test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.count_matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.count_matrix Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,40 @@
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b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,8 @@
+bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm
+1 TRINITY_DN2_c3_g1_i1 202 0.000000 0 0 0.000000 0.000000 0.000000e00 0.000000e00 0.000000e00 0.000000e00 0.000000e00 F 0.000000e+00
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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
+6 TRINITY_DN2_c2_g1_i1 240 240.000000 1 1 1.000000 1.000000 0.000000e00 0.000000e00 3.787879e05 3.787879e05 3.787879e05 T 6.017811e+04
+7 TRINITY_DN3_c0_g1_i1 216 0.000000 0 0 0.000000 0.000000 0.000000e00 0.000000e00 0.000000e00 0.000000e00 0.000000e00 F 0.000000e+00
b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,8 @@
+bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm
+1 TRINITY_DN0_c0_g1_i1 380 109.247050 5 5 5.000000 17.391774 0.000000e+00 0.000000e+00 4.160711e+06 4.160711e+06 4.160711e+06 T 6.610131e+05
+2 TRINITY_DN2_c0_g1_i1 279 0.000000 0 0 0.000000 0.000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 F 0.000000e+00
+3 TRINITY_DN2_c1_g1_i1 240 240.000000 1 1 1.000000 1.000000 0.000000e+00 0.000000e+00 3.787879e+05 3.787879e+05 3.787879e+05 T 6.017811e+04
+4 TRINITY_DN1_c0_g1_i1 229 0.000000 0 0 0.000000 0.000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 F 0.000000e+00
+5 TRINITY_DN3_c0_g1_i1 216 0.000000 0 0 0.000000 0.000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 F 0.000000e+00
+6 TRINITY_DN2_c3_g1_i1 202 0.000000 0 0 0.000000 0.000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 F 0.000000e+00
+7 TRINITY_DN2_c2_g1_i1 541 259.008053 5 5 5.000000 10.443691 0.000000e+00 0.000000e+00 1.754947e+06 1.754947e+06 1.754947e+06 T 2.788088e+05
b
diff -r 000000000000 -r 64094e19077d test-data/count/express_bowtie/sample_A
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/sample_A Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,8 @@
+bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm
+NA TRINITY_DN3_c0_g1 216.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0
+NA TRINITY_DN2_c2_g1 240.00 240.00 NA NA NA 1.00 NA NA 378787.90 NA NA NA 60178.11
+NA TRINITY_DN2_c3_g1 202.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0
+NA TRINITY_DN0_c0_g1 229.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0
+NA TRINITY_DN2_c0_g1 279.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0
+NA TRINITY_DN1_c0_g1 380.00 109.25 NA NA NA 17.39 NA NA 4160711.00 NA NA NA 661013.1
+NA TRINITY_DN2_c1_g1 541.00 259.01 NA NA NA 10.44 NA NA 1754947.00 NA NA NA 278808.8
b
diff -r 000000000000 -r 64094e19077d test-data/count/express_bowtie/sample_B
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/sample_B Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,8 @@
+bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm
+NA TRINITY_DN3_c0_g1 216.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0
+NA TRINITY_DN2_c1_g1 240.00 240.00 NA NA NA 1.00 NA NA 378787.90 NA NA NA 60178.11
+NA TRINITY_DN2_c3_g1 202.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0
+NA TRINITY_DN0_c0_g1 380.00 109.25 NA NA NA 17.39 NA NA 4160711.00 NA NA NA 661013.1
+NA TRINITY_DN1_c0_g1 229.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0
+NA TRINITY_DN2_c0_g1 279.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0
+NA TRINITY_DN2_c2_g1 541.00 259.01 NA NA NA 10.44 NA NA 1754947.00 NA NA NA 278808.8
b
diff -r 000000000000 -r 64094e19077d test-data/count/kallisto/abundance.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/kallisto/abundance.tsv Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,8 @@
+target_id length eff_length est_counts tpm
+TRINITY_DN1_c0_g1_i1 380 133.091 13 114025
+TRINITY_DN0_c0_g1_i1 229 31.75 7 257370
+TRINITY_DN2_c0_g1_i1 279 55.7143 1 20952.6
+TRINITY_DN2_c1_g1_i1 541 279.667 15 62611.6
+TRINITY_DN2_c2_g1_i1 240 42.75 4 109227
+TRINITY_DN2_c3_g1_i1 202 19 0 0
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b
diff -r 000000000000 -r 64094e19077d test-data/count/kallisto/abundance.tsv.genes
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/kallisto/abundance.tsv.genes Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,8 @@
+target_id length eff_length est_counts tpm
+TRINITY_DN3_c0_g1 216.00 18.75 7.00 435814.00
+TRINITY_DN2_c2_g1 240.00 42.75 4.00 109227.00
+TRINITY_DN2_c3_g1 202.00 19.00 0.00 0.00
+TRINITY_DN0_c0_g1 229.00 31.75 7.00 257370.00
+TRINITY_DN2_c0_g1 279.00 55.71 1.00 20952.60
+TRINITY_DN1_c0_g1 380.00 133.09 13.00 114025.00
+TRINITY_DN2_c1_g1 541.00 279.67 15.00 62611.60
b
diff -r 000000000000 -r 64094e19077d test-data/count/kallisto/abundance_B.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/kallisto/abundance_B.tsv Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,8 @@
+target_id length eff_length est_counts tpm
+TRINITY_DN1_c0_g1_i1 229 31.75 7 257370
+TRINITY_DN0_c0_g1_i1 380 133.091 13 114025
+TRINITY_DN2_c0_g1_i1 279 55.7143 1 20952.6
+TRINITY_DN2_c2_g1_i1 541 279.667 15 62611.6
+TRINITY_DN2_c1_g1_i1 240 42.75 4 109227
+TRINITY_DN2_c3_g1_i1 202 19 0 0
+TRINITY_DN3_c0_g1_i1 216 18.75 7 435814
b
diff -r 000000000000 -r 64094e19077d test-data/count/kallisto/abundance_B.tsv.genes
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/kallisto/abundance_B.tsv.genes Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,8 @@
+target_id length eff_length est_counts tpm
+TRINITY_DN3_c0_g1 216.00 18.75 7.00 435814.00
+TRINITY_DN2_c1_g1 240.00 42.75 4.00 109227.00
+TRINITY_DN2_c3_g1 202.00 19.00 0.00 0.00
+TRINITY_DN0_c0_g1 380.00 133.09 13.00 114025.00
+TRINITY_DN2_c0_g1 279.00 55.71 1.00 20952.60
+TRINITY_DN1_c0_g1 229.00 31.75 7.00 257370.00
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b
diff -r 000000000000 -r 64094e19077d test-data/count/matrix_express_bowtie/matrix.TMM.EXPR.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_express_bowtie/matrix.TMM.EXPR.matrix Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,8 @@
+ sample_A.tsv sample_B.tsv
+TRINITY_DN2_c1_g1_i1 278808.8 60178.11
+TRINITY_DN1_c0_g1_i1 0 0
+TRINITY_DN2_c2_g1_i1 60178.11 278808.8
+TRINITY_DN2_c0_g1_i1 0 0
+TRINITY_DN3_c0_g1_i1 0 0
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+TRINITY_DN0_c0_g1_i1 661013.1 661013.1
b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,8 @@
+ sample_A.tsv sample_B.tsv
+TRINITY_DN2_c1_g1_i1 278808.8 60178.11
+TRINITY_DN1_c0_g1_i1 0 0
+TRINITY_DN2_c2_g1_i1 60178.11 278808.8
+TRINITY_DN2_c0_g1_i1 0 0
+TRINITY_DN3_c0_g1_i1 0 0
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+TRINITY_DN0_c0_g1_i1 661013.1 661013.1
b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -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
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+TRINITY_DN0_c0_g1_i1 17.391774 17.391774
b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -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 64094e19077d 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 Thu Jun 14 03:12:34 2018 -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 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,8 @@
+ sample_A.tsv sample_B.tsv
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+TRINITY_DN4_c0_g1 0.00 0.00
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+TRINITY_DN3_c2_g1 1.00 5.00
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b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,8 @@
+ sample_A.tsv sample_B.tsv
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+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 64094e19077d 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 Thu Jun 14 03:12:34 2018 -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 64094e19077d 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 Thu Jun 14 03:12:34 2018 -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 64094e19077d 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 Thu Jun 14 03:12:34 2018 -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 64094e19077d 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 Thu Jun 14 03:12:34 2018 -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 64094e19077d 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 Thu Jun 14 03:12:34 2018 -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
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b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -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 64094e19077d 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 Thu Jun 14 03:12:34 2018 -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 64094e19077d 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 Thu Jun 14 03:12:34 2018 -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
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diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -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
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+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
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diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -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
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b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,8 @@
+transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct
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+TRINITY_DN1_c0_g1_i1 TRINITY_DN1_c0_g1 380 123.91 5.00 329523.81 3668378.58 100.00
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+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 64094e19077d 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 Thu Jun 14 03:12:34 2018 -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
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b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -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
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b
diff -r 000000000000 -r 64094e19077d test-data/count/rsem_bowtie2/RSEM.isoforms.results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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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
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b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -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
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b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -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
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b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,8 @@
+gene_id transcript_id(s) length effective_length expected_count TPM FPKM
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+TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 229.00 10.58 0.00 0.00 0.00
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b
diff -r 000000000000 -r 64094e19077d test-data/count/salmon/sample_A
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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b
@@ -0,0 +1,8 @@
+Name Length EffectiveLength TPM NumReads
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+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
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b
diff -r 000000000000 -r 64094e19077d test-data/count/salmon/sample_B
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/salmon/sample_B Thu Jun 14 03:12:34 2018 -0400
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 64094e19077d test-data/count/samples.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/samples.txt Thu Jun 14 03:12:34 2018 -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 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,41 @@
+gene_id length
+TR24|c0_g1_i1 290.00
+TR2779|c0_g1_i1 186.00
+TR127|c1_g1_i1 229.00
+TR2107|c1_g1_i1 259.00
+TR2011|c5_g1_i1 211.00
+TR4163|c0_g1_i1 368.00
+TR5055|c0_g2_i1 236.00
+TR1449|c0_g1_i1 196.00
+TR1982|c2_g1_i1 227.00
+TR1859|c3_g1_i1 220.00
+TR1492|c0_g1_i2 195.00
+TR1122|c0_g1_i1 222.00
+TR2278|c0_g1_i1 497.00
+TR4084|c0_g1_i1 295.00
+TR4761|c0_g1_i1 289.00
+TR3638|c0_g1_i1 247.00
+TR2090|c0_g1_i1 220.00
+TR3854|c0_g1_i1 178.00
+TR131|c0_g1_i1 232.00
+TR5075|c0_g1_i1 213.00
+TR2182|c3_g2_i6 221.44
+TR3788|c0_g1_i1 217.00
+TR4859|c0_g1_i1 226.00
+TR2487|c0_g1_i1 386.00
+TR2122|c0_g2_i2 145.00
+TR4277|c0_g1_i1 466.00
+TR3091|c0_g1_i1 222.00
+TR2130|c1_g3_i1 220.00
+TR3807|c0_g1_i1 226.00
+TR1894|c2_g1_i1 221.00
+TR5212|c0_g1_i1 264.00
+TR939|c0_g1_i1 296.00
+TR1891|c0_g1_i1 115.00
+TR2672|c0_g1_i1 214.00
+TR2844|c0_g1_i1 166.00
+TR1837|c2_g1_i1 221.00
+TR1678|c0_g1_i1 221.00
+TR3249|c0_g1_i1 221.00
+TR1479|c0_g1_i1 136.00
+TR4669|c0_g2_i1 136.00
b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
b
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'
b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
[
@@ -0,0 +1,34 @@
+>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
b
diff -r 000000000000 -r 64094e19077d test-data/filtered/Trinity_filtered_hi_iso.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filtered/Trinity_filtered_hi_iso.fasta Thu Jun 14 03:12:34 2018 -0400
[
@@ -0,0 +1,45 @@
+>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA
+ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC
+AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG
+AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA
+AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
+GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
+TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
+TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
b
diff -r 000000000000 -r 64094e19077d 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 Thu Jun 14 03:12:34 2018 -0400
[
@@ -0,0 +1,45 @@
+>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA
+ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC
+AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG
+AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA
+AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
+GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
+TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
+TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
b
diff -r 000000000000 -r 64094e19077d test-data/filtered/counts.matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filtered/counts.matrix Thu Jun 14 03:12:34 2018 -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 64094e19077d test-data/norm/Trinity.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/norm/Trinity.fasta Thu Jun 14 03:12:34 2018 -0400
[
@@ -0,0 +1,46 @@
+>TRINITY_DN1_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2]
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN0_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2]
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2]
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA
+ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC
+AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG
+AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA
+AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2]
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2]
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
+GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
+TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
+TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2]
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2]
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
+
b
diff -r 000000000000 -r 64094e19077d test-data/norm/Trinity_paired_unmerged_1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/norm/Trinity_paired_unmerged_1.fasta Thu Jun 14 03:12:34 2018 -0400
[
@@ -0,0 +1,14 @@
+>TRINITY_DN2_c0_g1_i1 len=229 path=[0:0-228]
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN1_c0_g1_i1 len=380 path=[0:0-379]
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATGTATATGGTACAGATGTAAAG
+>TRINITY_DN3_c0_g1_i1 len=669 path=[0:0-668]
+GCTGCATCAGACCAAGATGAAAGCATAGTAGAACTTGCATTTCAGACAACAGGGCACATTGTCACTCTTGTATTTGAAAAACACTTTCCGGCCACCATTGATTCTTTCCAGGATGCAGTGAAGTGTTTGTCTGAATTCACATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTG
+>TRINITY_DN3_c0_g2_i1 len=279 path=[0:0-278]
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN3_c0_g3_i1 len=240 path=[0:0-239]
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGAGTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGCTACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN3_c0_g4_i1 len=202 path=[0:0-201]
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACCAA
+>TRINITY_DN0_c0_g1_i1 len=216 path=[0:0-215]
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
b
diff -r 000000000000 -r 64094e19077d test-data/norm/Trinity_paired_unmerged_1.map
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/norm/Trinity_paired_unmerged_1.map Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,7 @@
+TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1
+TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1
+TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1
+TRINITY_DN3_c0_g2 TRINITY_DN3_c0_g2_i1
+TRINITY_DN3_c0_g3 TRINITY_DN3_c0_g3_i1
+TRINITY_DN3_c0_g4 TRINITY_DN3_c0_g4_i1
+TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1
b
diff -r 000000000000 -r 64094e19077d test-data/raw/Trinity.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw/Trinity.fasta Thu Jun 14 03:12:34 2018 -0400
[
@@ -0,0 +1,45 @@
+>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2]
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2]
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2]
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA
+ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC
+AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG
+AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA
+AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2]
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2]
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
+GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
+TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
+TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2]
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2]
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
b
diff -r 000000000000 -r 64094e19077d test-data/raw/Trinity_single_unmerged_1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw/Trinity_single_unmerged_1.fasta Thu Jun 14 03:12:34 2018 -0400
[
@@ -0,0 +1,2 @@
+>TRINITY_DN0_c0_g1_i1 len=226 path=[0:0-225]
+CTTTACATCTGTACCATATACATATCCACCTGAAAACATTTTCTACATCCACTGTTATATGGAATGCTTGATAAGCTTTTCATTCTAACCATCAGAGCACAGTTCACAGTATGAATACATTTCCAGTAAATCTAACCTCCCAAAACCATGCCAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATCTACATCAAGCCCCGCCACCC
b
diff -r 000000000000 -r 64094e19077d test-data/raw/Trinity_single_unmerged_1.map
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw/Trinity_single_unmerged_1.map Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,1 @@
+TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1
b
diff -r 000000000000 -r 64094e19077d test-data/raw/map.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw/map.tsv Thu Jun 14 03:12:34 2018 -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 64094e19077d test-data/reads.left.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.left.fq Thu Jun 14 03:12:34 2018 -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 64094e19077d test-data/reads.right.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.right.fq Thu Jun 14 03:12:34 2018 -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 64094e19077d test-data/samples.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samples.tsv Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,4 @@
+ConditionA CondA_replicate1
+ConditionA CondA_replicate2
+ConditionB CondB_replicate1
+ConditionB CondB_replicate2
b
diff -r 000000000000 -r 64094e19077d test-data/supertranscripts/trinity_genes.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/supertranscripts/trinity_genes.fasta Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,14 @@
+>TRINITY_DN1_c0_g1
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATGTATATGGTACAGATGTAAAG
+>TRINITY_DN0_c0_g1
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c0_g1
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN2_c1_g1
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTG
+>TRINITY_DN2_c2_g1
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGAGTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGCTACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN2_c3_g1
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
b
diff -r 000000000000 -r 64094e19077d test-data/supertranscripts/trinity_genes.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/supertranscripts/trinity_genes.gtf Thu Jun 14 03:12:34 2018 -0400
b
@@ -0,0 +1,14 @@
+TRINITY_DN1_c0_g1 Trinity_gene exon 1 380 . + . gene_id "TRINITY_DN1_c0_g1"; transcript_id "TRINITY_DN1_c0_g1_i1"
+
+TRINITY_DN0_c0_g1 Trinity_gene exon 1 229 . + . gene_id "TRINITY_DN0_c0_g1"; transcript_id "TRINITY_DN0_c0_g1_i1"
+
+TRINITY_DN2_c0_g1 Trinity_gene exon 1 279 . + . gene_id "TRINITY_DN2_c0_g1"; transcript_id "TRINITY_DN2_c0_g1_i1"
+
+TRINITY_DN2_c1_g1 Trinity_gene exon 1 541 . + . gene_id "TRINITY_DN2_c1_g1"; transcript_id "TRINITY_DN2_c1_g1_i1"
+
+TRINITY_DN2_c2_g1 Trinity_gene exon 1 240 . + . gene_id "TRINITY_DN2_c2_g1"; transcript_id "TRINITY_DN2_c2_g1_i1"
+
+TRINITY_DN2_c3_g1 Trinity_gene exon 1 202 . + . gene_id "TRINITY_DN2_c3_g1"; transcript_id "TRINITY_DN2_c3_g1_i1"
+
+TRINITY_DN3_c0_g1 Trinity_gene exon 1 216 . + . gene_id "TRINITY_DN3_c0_g1"; transcript_id "TRINITY_DN3_c0_g1_i1"
+