Mercurial > repos > iuc > trinity_gene_to_trans_map

changeset 2:2d2e0769164c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
author iuc
date Mon, 21 Nov 2016 09:22:49 -0500
parents 405e436ec8b3
children 4ffe49475169
files 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.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/trinotate/genes.lengths.txt test-data/count/trinotate/go_annotations.txt
diffstat 25 files changed, 169 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,7 @@
+id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR4277|c0_g1_i1	3852.97388871986	161.116814813422	2007.04535176664	-4.57259674791206	0.121601866332754	-37.6030145409076	0	0	4466.00	4701.00	4284.00	118.00	134.00	164.00	172.00	162.00	170.00
+TR4761|c0_g1_i1	1645.20640957447	193.196157329029	919.201283451752	-3.08847487551254	0.143642016580712	-21.5011940728159	1.51733402752078e-102	1.66906743027286e-101	2089.00	1746.00	1875.00	155.00	174.00	165.00	394.00	389.00	406.00
+TR2107|c1_g1_i1	48.9228907410258	7.40521775805688	28.1640542495414	-2.6949883047084	0.431525668867458	-6.24525607429428	4.23106352657394e-10	1.55138995974378e-09	59.00	65.00	47.00	6.00	6.00	7.00	3.00	1.00	2.00
+TR2672|c0_g1_i1	18.3155337236093	2.26581902751323	10.2906763755613	-2.88818323474529	0.724350842979802	-3.98727117216294	6.68376171815065e-05	0.000157545811927837	14.00	29.00	22.00	0.00	4.00	2.00	14.00	4.00	7.00
+TR127|c1_g1_i1	13.461799216177	1.21881296083961	7.34030608850831	-3.33218181130749	0.914685635912973	-3.64298036448506	0.000269499403689035	0.000576210779000196	9.00	23.00	16.00	2.00	0.00	1.00	3.00	1.00	1.00
+TR5055|c0_g2_i1	23.3590211688541	5.52768338415684	14.4433522765055	-2.04478780320925	0.562727305023446	-3.63370994255211	0.00027937492315161	0.000576210779000196	36.00	17.00	27.00	4.00	7.00	3.00	4.00	4.00	11.00
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.depleted	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR	under_represented_FDR
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,4 @@
+id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR131|c0_g1_i1	26.1866396538608	1340.30918254958	683.247911101723	5.67372481552909	0.187406695960058	30.274931140872	2.45144211418965e-201	4.04487948841292e-200	32.00	28.00	31.00	1001.00	1233.00	1208.00	1486.00	1492.00	1457.00
+TR3091|c0_g1_i1	16.7444693227929	328.569936894811	172.657203108802	4.29039998257063	0.240421038467916	17.8453599980735	3.14072644239509e-71	2.59109931497595e-70	22.00	17.00	19.00	250.00	308.00	284.00	333.00	343.00	316.00
+TR3788|c0_g1_i1	19.5075441237117	134.95369713876	77.2306206312357	2.77038513264018	0.262760026053246	10.5434040871909	5.44900939296595e-26	2.56881871382681e-25	17.00	30.00	22.00	91.00	132.00	125.00	32.00	22.00	27.00
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset.GOseq.depleted	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR	under_represented_FDR
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset.GOseq.enriched	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,7 @@
+id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR4277|c0_g1_i1	4705.34614971641	162.902721493704	2434.12443560506	-4.84860951090545	0.124597307945428	-38.9142397284305	0	0	4466.00	4701.00	4284.00	118.00	134.00	164.00	172.00	162.00	170.00
+TR4761|c0_g1_i1	2012.6141923276	384.620292965437	1198.61724264652	-2.38450946693381	0.143863830576436	-16.5747669680385	1.06073316501088e-61	1.34359534234711e-60	2089.00	1746.00	1875.00	155.00	174.00	165.00	394.00	389.00	406.00
+TR2107|c1_g1_i1	59.5986596731862	1.89840873462066	30.7485342039034	-4.81058600791914	0.641850436461167	-7.49487066557473	6.63637683134955e-14	2.29256654173894e-13	59.00	65.00	47.00	6.00	6.00	7.00	3.00	1.00	2.00
+TR127|c1_g1_i1	16.3791628279609	1.58772512712498	8.98344397754296	-3.19771077466237	0.834376974262452	-3.83245328346816	0.00012687169720824	0.000267840249661839	9.00	23.00	16.00	2.00	0.00	1.00	3.00	1.00	1.00
+TR1894|c2_g1_i1	16.2826445742552	1.67571344127509	8.97917900776516	-3.15659686337855	0.834779400611257	-3.7813545244015	0.00015597736029041	0.000307529893573321	21.00	14.00	11.00	1.00	2.00	5.00	1.00	3.00	1.00
+TR5055|c0_g2_i1	28.6665933385886	6.05959103586122	17.3630921872249	-2.17768048931004	0.577307428800381	-3.77213314894485	0.000161857838722801	0.000307529893573321	36.00	17.00	27.00	4.00	7.00	3.00	4.00	4.00	11.00
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.depleted	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR	under_represented_FDR
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,2 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR	go_term
+GO:0008270	0.0469428206943769	0.996332779511344	3	6	zinc ion binding	MF	0.790651800018629	MF zinc ion binding
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,5 @@
+id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR131|c0_g1_i1	32.0461070493257	1436.30905989883	734.177583474076	5.48367743370229	0.196017912869615	27.9753893581648	3.23827538807456e-172	6.15272323734167e-171	32.00	28.00	31.00	1001.00	1233.00	1208.00	1486.00	1492.00	1457.00
+TR3091|c0_g1_i1	20.4914097091341	321.651020117047	171.071214913091	3.96886910507283	0.256323110469072	15.4838519937191	4.45952081812589e-54	4.2365447772196e-53	22.00	17.00	19.00	250.00	308.00	284.00	333.00	343.00	316.00
+TR2779|c0_g1_i1	191.51955185349	1058.15934185376	624.839446853626	2.46616535412611	0.177102083131526	13.9251064161374	4.4587691300744e-44	3.38866453885655e-43	186.00	137.00	217.00	147.00	186.00	197.00	1088.00	1094.00	1086.00
+TR5075|c0_g1_i1	19.3833722195684	136.98672801182	78.1850501156942	2.80049241151413	0.293976352213923	9.52625063350759	1.63066468983638e-21	8.85217974482605e-21	13.00	22.00	21.00	6.00	8.00	10.00	163.00	121.00	142.00
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.depleted	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR	under_represented_FDR
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.enriched	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,1 @@
+id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,3 @@
+id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR2779|c0_g1_i1	195.849684476753	966.924129135581	581.386906806167	2.25621220756415	0.156114979193812	14.4522467940961	2.42639762934434e-47	5.82335431042642e-46	186.00	137.00	217.00	147.00	186.00	197.00	1088.00	1094.00	1086.00
+TR24|c0_g1_i1	39.3724575919554	183.288101009647	111.330279300801	2.11680322693425	0.240338854880295	8.80757806717753	1.27878744153922e-18	7.67272464923531e-18	90.00	67.00	85.00	36.00	35.00	34.00	222.00	196.00	201.00
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.depleted	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR	under_represented_FDR
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.enriched	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/results.matrix	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,14 @@
+	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR24|c0_g1_i1	90.00	67.00	85.00	36.00	35.00	34.00	222.00	196.00	201.00
+TR4277|c0_g1_i1	4466.00	4701.00	4284.00	118.00	134.00	164.00	172.00	162.00	170.00
+TR2779|c0_g1_i1	186.00	137.00	217.00	147.00	186.00	197.00	1088.00	1094.00	1086.00
+TR2672|c0_g1_i1	14.00	29.00	22.00	0.00	4.00	2.00	14.00	4.00	7.00
+TR127|c1_g1_i1	9.00	23.00	16.00	2.00	0.00	1.00	3.00	1.00	1.00
+TR2107|c1_g1_i1	59.00	65.00	47.00	6.00	6.00	7.00	3.00	1.00	2.00
+TR5055|c0_g2_i1	36.00	17.00	27.00	4.00	7.00	3.00	4.00	4.00	11.00
+TR3091|c0_g1_i1	22.00	17.00	19.00	250.00	308.00	284.00	333.00	343.00	316.00
+TR4761|c0_g1_i1	2089.00	1746.00	1875.00	155.00	174.00	165.00	394.00	389.00	406.00
+TR131|c0_g1_i1	32.00	28.00	31.00	1001.00	1233.00	1208.00	1486.00	1492.00	1457.00
+TR5075|c0_g1_i1	13.00	22.00	21.00	6.00	8.00	10.00	163.00	121.00	142.00
+TR1894|c2_g1_i1	21.00	14.00	11.00	1.00	2.00	5.00	1.00	3.00	1.00
+TR3788|c0_g1_i1	17.00	30.00	22.00	91.00	132.00	125.00	32.00	22.00	27.00
Binary file test-data/count/analyze_diff_expr/results.matrix.RData has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/results.matrix.log2.centered.dat	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,14 @@
+wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR24|c0_g1_i1	0.106533882165825	-0.313797916782532	0.025003996669227	-1.19180739240392	-1.23133575659056	-1.2719777410879	1.39963914188743	1.22079106142351	1.25695072471892
+TR4277|c0_g1_i1	3.24415794782388	3.31812623217364	3.18414689752048	-1.98611482817144	-1.80411699442855	-1.51461037723356	-1.44630436384266	-1.5322044372483	-1.46308007659348
+TR2779|c0_g1_i1	-0.795433018475884	-1.23380302158535	-0.574143153586594	-1.13287411273457	-0.795433018475884	-0.712970858283911	1.74646076035339	1.75438767612502	1.74380874666379
+TR2672|c0_g1_i1	0.965440325233136	1.96544032523314	1.58211168568163	-2.94145027037538	-0.619522175488021	-1.35648776965423	0.965440325233136	-0.619522175488021	0.0585497296246169
+TR127|c1_g1_i1	1.25755965737847	2.52059406321227	2.02309440374145	-0.479405936787734	-2.06436843750889	-1.06436843750889	-0.0643684375088904	-1.06436843750889	-1.06436843750889
+TR2107|c1_g1_i1	2.49178842221691	2.62929194596684	2.16986032732955	-0.607747251334006	-0.607747251334006	-0.41510217339161	-1.41510217339161	-2.41510217339161	-1.83013967267045
+TR5055|c0_g2_i1	1.90528891290538	0.865760548718745	1.50319046933404	-0.982236357836205	-0.304164452723568	-1.30416445272357	-0.982236357836205	-0.982236357836205	0.280798047997588
+TR3091|c0_g1_i1	-2.42438780178849	-2.77802475640319	-2.62602166295814	1.02359379610527	1.32351327005887	1.20686835120661	1.43575453462855	1.4783149968566	1.36038927229391
+TR4761|c0_g1_i1	2.06406810079911	1.80544476674762	1.90822498634624	-1.67981690730689	-1.51400801433681	-1.59017969482221	-0.339510283104669	-0.357888812419525	-0.296334141902888
+TR131|c0_g1_i1	-3.50802026981862	-3.6944333940495	-3.55241438917708	1.41625240401813	1.71671228997234	1.68718414007205	1.98577454287534	1.99158406095747	1.95736061514986
+TR5075|c0_g1_i1	-1.04544737992556	-0.329240345926152	-0.393370683345868	-2.04544737992556	-1.68287730054085	-1.39337068334587	2.50474970263492	2.07793503557972	2.30706903479522
+TR1894|c2_g1_i1	2.11263053903627	1.56008951600749	1.23816142112012	-1.34680107960103	-0.761838578879876	0.238161421120124	-1.34680107960103	-0.346801079601032	-1.34680107960103
+TR3788|c0_g1_i1	-1.22775484082629	-0.443483531881724	-0.874117886211586	1.12588211378841	1.65760259323259	1.57960008123132	-0.353285722910146	-0.874117886211586	-0.590324920210995
Binary file test-data/count/analyze_diff_expr/results.matrix.log2.centered.genes_vs_samples_heatmap.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/results.matrix.log2.dat	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,14 @@
+wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR24|c0_g1_i1	6.5077946401987	6.08746284125034	6.4262647547021	5.20945336562895	5.16992500144231	5.12928301694497	7.8008998999203	7.62205181945638	7.65821148275179
+TR4277|c0_g1_i1	12.1250905393033	12.199058823653	12.0650794889999	6.89481776330794	7.07681559705083	7.36632221424582	7.43462822763672	7.34872815423108	7.4178525148859
+TR2779|c0_g1_i1	7.54689445988764	7.10852445677817	7.76818432477693	7.20945336562895	7.54689445988764	7.62935662007961	10.0887882387169	10.0967151544885	10.0861362250273
+TR2672|c0_g1_i1	3.90689059560852	4.90689059560852	4.52356195605701	0	2.32192809488736	1.58496250072116	3.90689059560852	2.32192809488736	3
+TR127|c1_g1_i1	3.32192809488736	4.58496250072116	4.08746284125034	1.58496250072116	0	1	2	1	1
+TR2107|c1_g1_i1	5.90689059560852	6.04439411935845	5.58496250072116	2.8073549220576	2.8073549220576	3	2	1	1.58496250072116
+TR5055|c0_g2_i1	5.20945336562895	4.16992500144231	4.8073549220576	2.32192809488736	3	2	2.32192809488736	2.32192809488736	3.58496250072116
+TR3091|c0_g1_i1	4.52356195605701	4.16992500144231	4.32192809488736	7.97154355395077	8.27146302790437	8.1548181090521	8.38370429247405	8.4262647547021	8.30833903013941
+TR4761|c0_g1_i1	11.0292872269682	10.7706638929168	10.8734441125154	7.28540221886225	7.45121111183233	7.37503943134692	8.62570884306447	8.60733031374961	8.66888498426625
+TR131|c0_g1_i1	5.04439411935845	4.85798099512757	5	9.96866679319521	10.2691266791494	10.2395985292491	10.5381889320524	10.5439984501345	10.5097750043269
+TR5075|c0_g1_i1	3.8073549220576	4.52356195605701	4.4594316186373	2.8073549220576	3.16992500144231	3.4594316186373	7.35755200461808	6.93073733756289	7.15987133677839
+TR1894|c2_g1_i1	4.4594316186373	3.90689059560852	3.58496250072116	1	1.58496250072116	2.58496250072116	1	2	1
+TR3788|c0_g1_i1	4.16992500144231	4.95419631038687	4.52356195605701	6.52356195605701	7.05528243550119	6.97727992349992	5.04439411935845	4.52356195605701	4.8073549220576
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor.dat	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,10 @@
+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
+wt_37_2	1	0.968650822800566	0.985499030254524	0.457364683078012	0.443497697874748	0.451451348748615	0.41961787977306	0.444203836374748	0.448348619980356
+wt_37_3	0.968650822800566	1	0.98879028662025	0.400031307625771	0.378330685571456	0.396636302989378	0.39057945325073	0.383299487197462	0.388022080096891
+wt_37_1	0.985499030254524	0.98879028662025	1	0.452638132682111	0.434834315692609	0.44176483058741	0.461437515072935	0.462172448553839	0.473652431554024
+wt_GSNO_3	0.457364683078012	0.400031307625771	0.452638132682111	1	0.965144031362199	0.979742518682039	0.844139129634192	0.862862111399854	0.857171072391268
+wt_GSNO_1	0.443497697874748	0.378330685571456	0.434834315692609	0.965144031362199	1	0.983818328020852	0.858668155107621	0.871693931267863	0.876908826664397
+wt_GSNO_2	0.451451348748615	0.396636302989378	0.44176483058741	0.979742518682039	0.983818328020852	1	0.854388461031158	0.878292745544781	0.861156659158544
+wt_ph8_3	0.41961787977306	0.39057945325073	0.461437515072935	0.844139129634192	0.858668155107621	0.854388461031158	1	0.984071267766826	0.98764423106737
+wt_ph8_1	0.444203836374748	0.383299487197462	0.462172448553839	0.862862111399854	0.871693931267863	0.878292745544781	0.984071267766826	1	0.989191009161984
+wt_ph8_2	0.448348619980356	0.388022080096891	0.473652431554024	0.857171072391268	0.876908826664397	0.861156659158544	0.98764423106737	0.989191009161984	1
Binary file test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor_matrix.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/trinotate/genes.lengths.txt	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,40 @@
+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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/trinotate/go_annotations.txt	Mon Nov 21 09:22:49 2016 -0500
@@ -0,0 +1,39 @@
+TR24|c0_g1_i1	GO:0003674,GO:0003824,GO:0003865,GO:0005575,GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229,GO:0016491,GO:0016627,GO:0031090,GO:0033765,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0071704,GO:0098588,GO:0098589,GO:1901360
+TR2779|c0_g1_i1	GO:0003674,GO:0003824,GO:0004596,GO:0005575,GO:0005634,GO:0005737,GO:0008080,GO:0016407,GO:0016410,GO:0016740,GO:0016746,GO:0016747,GO:0034212,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464
+TR127|c1_g1_i1	GO:0003674,GO:0003824,GO:0004310,GO:0004311,GO:0004659,GO:0005575,GO:0005789,GO:0006066,GO:0006629,GO:0006694,GO:0006720,GO:0008150,GO:0008152,GO:0008202,GO:0008299,GO:0008610,GO:0009058,GO:0009987,GO:0016020,GO:0016021,GO:0016125,GO:0016126,GO:0016491,GO:0016740,GO:0016765,GO:0031090,GO:0044237,GO:0044238,GO:0044249,GO:0044255,GO:0044281,GO:0044283,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0044711,GO:0044763,GO:0046165,GO:0051996,GO:0071704,GO:0098588,GO:0098589,GO:1901360,GO:1901362,GO:1901576,GO:1901615,GO:1901617
+TR2107|c1_g1_i1	GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175,GO:0004190,GO:0004518,GO:0004519,GO:0005488,GO:0006139,GO:0006259,GO:0006310,GO:0006725,GO:0006807,GO:0008150,GO:0008152,GO:0008233,GO:0009987,GO:0015074,GO:0016740,GO:0016772,GO:0016779,GO:0016787,GO:0016788,GO:0034061,GO:0034641,GO:0043167,GO:0043169,GO:0043170,GO:0044237,GO:0044238,GO:0044260,GO:0046483,GO:0046872,GO:0070001,GO:0070011,GO:0071704,GO:0090304,GO:0097159,GO:1901360,GO:1901363
+TR2011|c5_g1_i1	GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005737,GO:0006801,GO:0006810,GO:0006811,GO:0006812,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169,GO:0044237,GO:0044424,GO:0044464,GO:0044699,GO:0044710,GO:0044765,GO:0046872,GO:0046914,GO:0051234,GO:0055114,GO:0072593
+TR4163|c0_g1_i1	GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005634,GO:0005743,GO:0005829,GO:0006801,GO:0006873,GO:0006875,GO:0006878,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0010035,GO:0010038,GO:0016020,GO:0016530,GO:0016531,GO:0016532,GO:0019725,GO:0019866,GO:0030003,GO:0030234,GO:0031090,GO:0031966,GO:0042221,GO:0042592,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044237,GO:0044422,GO:0044424,GO:0044429,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0044763,GO:0046872,GO:0046914,GO:0046916,GO:0048878,GO:0050801,GO:0050896,GO:0051716,GO:0055065,GO:0055070,GO:0055076,GO:0055080,GO:0055082,GO:0055114,GO:0065007,GO:0065008,GO:0070887,GO:0071241,GO:0071248,GO:0072593
+TR5055|c0_g2_i1	GO:0003674,GO:0005488,GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872,GO:0046914
+TR1449|c0_g1_i1	GO:0003674,GO:0005488,GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872,GO:0046914
+TR1982|c2_g1_i1	GO:0003674,GO:0003824,GO:0003865,GO:0005575,GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229,GO:0016491,GO:0016627,GO:0031090,GO:0033765,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0071704,GO:0098588,GO:0098589,GO:1901360
+TR1859|c3_g1_i1	GO:0003676
+TR1492|c0_g1_i2	GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229
+TR1122|c0_g1_i1	GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234
+TR2278|c0_g1_i1	GO:0031090,GO:0033765
+TR4084|c0_g1_i1	GO:0003674,GO:0005488,GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872,GO:0046914
+TR4761|c0_g1_i1	GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234
+TR3638|c0_g1_i1	GO:0003865,GO:0005575,GO:0005783
+TR2090|c0_g1_i1	GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005634,GO:0005743,GO:0005829,GO:0006801,GO:0006873,GO:0006875,GO:0006878,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0010035,GO:0010038,GO:0016020,GO:0016530,GO:0016531,GO:0016532,GO:0019725,GO:0019866,GO:0030003,GO:0030234,GO:0031090,GO:0031966,GO:0042221,GO:0042592,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044237,GO:0044422,GO:0044424,GO:0044429,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0044763,GO:0046872,GO:0046914,GO:0046916,GO:0048878,GO:0050801,GO:0050896,GO:0051716,GO:0055065,GO:0055070,GO:0055076,GO:0055080,GO:0055082,GO:0055114,GO:0065007,GO:0065008,GO:0070887,GO:0071241,GO:0071248,GO:0072593
+TR3854|c0_g1_i1	GO:0003674,GO:0003824,GO:0003865,GO:0005575,GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229,GO:0016491,GO:0016627,GO:0031090,GO:0033765,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0071704,GO:0098588,GO:0098589,GO:1901360
+TR131|c0_g1_i1	GO:0031090,GO:0033765
+TR5075|c0_g1_i1	GO:0031090,GO:0033765
+TR2182|c3_g2_i6	GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175,GO:0004190,GO:0004518,GO:0004519,GO:0005488,GO:0006139
+TR3788|c0_g1_i1	GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229
+TR4859|c0_g1_i1	GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175,GO:0004190,GO:0004518,GO:0004519,GO:0005488,GO:0006139
+TR2487|c0_g1_i1	GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169
+TR2122|c0_g2_i2	GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872
+TR4277|c0_g1_i1	GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872
+TR3091|c0_g1_i1	GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169
+TR2130|c1_g3_i1	GO:0003674,GO:0003824,GO:0003865,GO:0005575,GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229,GO:0016491,GO:0016627,GO:0031090,GO:0033765,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0071704,GO:0098588,GO:0098589,GO:1901360
+TR3807|c0_g1_i1	GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005634,GO:0005743,GO:0005829,GO:0006801,GO:0006873,GO:0006875,GO:0006878,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0010035,GO:0010038,GO:0016020,GO:0016530,GO:0016531,GO:0016532,GO:0019725,GO:0019866,GO:0030003,GO:0030234,GO:0031090,GO:0031966,GO:0042221,GO:0042592,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044237,GO:0044422,GO:0044424,GO:0044429,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0044763,GO:0046872,GO:0046914,GO:0046916,GO:0048878,GO:0050801,GO:0050896,GO:0051716,GO:0055065,GO:0055070,GO:0055076,GO:0055080,GO:0055082,GO:0055114,GO:0065007,GO:0065008,GO:0070887,GO:0071241,GO:0071248,GO:0072593
+TR1894|c2_g1_i1	GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872
+TR5212|c0_g1_i1	GO:0003865,GO:0005575,GO:0005783
+TR939|c0_g1_i1	GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175,GO:0004190,GO:0004518,GO:0004519,GO:0005488,GO:0006139
+TR1891|c0_g1_i1	GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175
+TR2672|c0_g1_i1	GO:0003865,GO:0005575,GO:0005783
+TR2844|c0_g1_i1	GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234
+TR1837|c2_g1_i1	GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005737,GO:0006801,GO:0006810,GO:0006811,GO:0006812,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169,GO:0044237,GO:0044424,GO:0044464,GO:0044699,GO:0044710,GO:0044765,GO:0046872,GO:0046914,GO:0051234,GO:0055114,GO:0072593
+TR1678|c0_g1_i1	GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175
+TR3249|c0_g1_i1	GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175
+TR1479|c0_g1_i1	GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005737,GO:0006801,GO:0006810,GO:0006811,GO:0006812,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169,GO:0044237,GO:0044424,GO:0044464,GO:0044699,GO:0044710,GO:0044765,GO:0046872,GO:0046914,GO:0051234,GO:0055114,GO:0072593