Mercurial > repos > iuc > trinity_stats
changeset 0:b2ce45417d9e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,37 @@ +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. + +This tool uses the GALAXY_MEMORY_MB environmental variable to limit the its memory usage. If you use a supported cluster type, you just need to limit the memory in the destination section of the job_conf.xml file to the amount of available memory (in MB), for example with a Slurm cluster:: + + <destination id="cluster_high_mem" runner="slurm + <param id="nativeSpecification">--mem=1024</param> + </destination> + +If you cluster type does not support memory limit detection, you can also set manually the GALAXY_MEMORY_MB environmental variable in the destination section of the job_conf.xml file to the amount of available memory (in MB):: + + <?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">1024</env> + </destination> + </destinations> + </job_conf> + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,62 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">trinity</requirement> + <yield/> + </requirements> + </xml> + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">trinity</xref> + </xrefs> + </xml> + <token name="@TOOL_VERSION@">2.15.1</token> + <token name="@VERSION_SUFFIX@">0</token> + + <token name="@COMMAND_PAIRED_STRAND_JACCARD@"> + #if $pool.inputs.strand.is_strand_specific == 'true': + --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="select" label="Strand specific data"> + <option value="false">No</option> + <option value="true">Yes</option> + </param> + <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 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="is_strand_specific_f_r"> + <conditional name="strand"> + <param name="is_strand_specific" type="select" label="Strand specific data"> + <option value="false">No</option> + <option value="true">Yes</option> + </param> + <when value="false"/> + <when value="true"> + <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type"> + <option value="F">F</option> + <option value="R">R</option> + </param> + </when> + </conditional> + </xml> + + <xml name="citation"> + <citations> + <citation type="doi">10.1038/nbt.1883</citation> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/Trinity.map Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset Tue Aug 08 09:12:09 2023 +0000 @@ -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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 Tue Aug 08 09:12:09 2023 +0000 @@ -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_C2.0.DE.subset.GOseq.enriched Tue Aug 08 09:12:09 2023 +0000 @@ -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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 +TR3788|c0_g1_i1 17.00 30.00 22.00 91.00 132.00 125.00 32.00 22.00 27.00 +TR24|c0_g1_i1 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00 +TR3091|c0_g1_i1 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00 +TR2779|c0_g1_i1 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00 +TR2107|c1_g1_i1 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00 +TR4761|c0_g1_i1 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00 +TR5055|c0_g2_i1 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00 +TR5075|c0_g1_i1 13.00 22.00 21.00 6.00 8.00 10.00 163.00 121.00 142.00 +TR2672|c0_g1_i1 14.00 29.00 22.00 0.00 4.00 2.00 14.00 4.00 7.00 +TR4277|c0_g1_i1 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00 +TR127|c1_g1_i1 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 +TR131|c0_g1_i1 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00 +TR1894|c2_g1_i1 21.00 14.00 11.00 1.00 2.00 5.00 1.00 3.00 1.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/results.matrix.log2.centered.dat Tue Aug 08 09:12:09 2023 +0000 @@ -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 +TR3788|c0_g1_i1 -1.22775484082629 -0.443483531881724 -0.874117886211586 1.12588211378841 1.65760259323259 1.57960008123132 -0.353285722910146 -0.874117886211586 -0.590324920210995 +TR24|c0_g1_i1 0.106533882165825 -0.313797916782532 0.025003996669227 -1.19180739240392 -1.23133575659056 -1.2719777410879 1.39963914188743 1.22079106142351 1.25695072471892 +TR3091|c0_g1_i1 -2.42438780178849 -2.77802475640319 -2.62602166295814 1.02359379610527 1.32351327005887 1.20686835120661 1.43575453462855 1.4783149968566 1.36038927229391 +TR2779|c0_g1_i1 -0.795433018475884 -1.23380302158535 -0.574143153586594 -1.13287411273457 -0.795433018475884 -0.712970858283911 1.74646076035339 1.75438767612502 1.74380874666379 +TR2107|c1_g1_i1 2.49178842221691 2.62929194596684 2.16986032732955 -0.607747251334006 -0.607747251334006 -0.41510217339161 -1.41510217339161 -2.41510217339161 -1.83013967267045 +TR4761|c0_g1_i1 2.06406810079911 1.80544476674762 1.90822498634624 -1.67981690730689 -1.51400801433681 -1.59017969482221 -0.339510283104669 -0.357888812419525 -0.296334141902888 +TR5055|c0_g2_i1 1.90528891290538 0.865760548718745 1.50319046933404 -0.982236357836205 -0.304164452723568 -1.30416445272357 -0.982236357836205 -0.982236357836205 0.280798047997588 +TR5075|c0_g1_i1 -1.04544737992556 -0.329240345926152 -0.393370683345868 -2.04544737992556 -1.68287730054085 -1.39337068334587 2.50474970263492 2.07793503557972 2.30706903479522 +TR2672|c0_g1_i1 0.965440325233136 1.96544032523314 1.58211168568163 -2.94145027037538 -0.619522175488021 -1.35648776965423 0.965440325233136 -0.619522175488021 0.0585497296246169 +TR4277|c0_g1_i1 3.24415794782388 3.31812623217364 3.18414689752048 -1.98611482817144 -1.80411699442855 -1.51461037723356 -1.44630436384266 -1.5322044372483 -1.46308007659348 +TR127|c1_g1_i1 1.25755965737847 2.52059406321227 2.02309440374145 -0.479405936787734 -2.06436843750889 -1.06436843750889 -0.0643684375088904 -1.06436843750889 -1.06436843750889 +TR131|c0_g1_i1 -3.50802026981862 -3.6944333940495 -3.55241438917708 1.41625240401813 1.71671228997234 1.68718414007205 1.98577454287534 1.99158406095747 1.95736061514986 +TR1894|c2_g1_i1 2.11263053903627 1.56008951600749 1.23816142112012 -1.34680107960103 -0.761838578879876 0.238161421120124 -1.34680107960103 -0.346801079601032 -1.34680107960103
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/contig_exn50_statistic/ExN50.stats Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,5 @@ +Ex ExN50 num_transcripts +33 541 1 +67 541 2 +99 380 3 +100 279 7
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/contig_exn50_statistic/Trinity.fasta Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,46 @@ +>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] +CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG +CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC +AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT +ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG +GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG +AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG +TATATGGTACAGATGTAAAG +>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT +TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT +ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA +TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC +>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] +TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA +ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC +AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG +AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA +AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA +>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT +TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA +TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT +TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT +AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT +ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA +AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC +CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG +GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT +G +>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] +ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA +GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC +TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG +TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC +>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] +GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC +AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC +CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC +ATACATGATTCTATTCAACCAA +>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG +CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT +ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA +TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/contig_exn50_statistic/matrix.TMM.EXPR.matrix Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/define_clusters_by_cutting_tree/subcluster_1_log2_medianCentered_fpkm.matrix Tue Aug 08 09:12:09 2023 +0000 @@ -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 +TR3788|c0_g1_i1 -1.22775484082629 -0.443483531881724 -0.874117886211586 -0.353285722910146 -0.874117886211586 -0.590324920210995 1.12588211378841 1.65760259323259 1.57960008123132 +TR24|c0_g1_i1 0.106533882165825 -0.313797916782532 0.025003996669227 1.39963914188743 1.22079106142351 1.25695072471892 -1.19180739240392 -1.23133575659056 -1.2719777410879 +TR3091|c0_g1_i1 -2.42438780178849 -2.77802475640319 -2.62602166295814 1.43575453462855 1.4783149968566 1.36038927229391 1.02359379610527 1.32351327005887 1.20686835120661 +TR2779|c0_g1_i1 -0.795433018475884 -1.23380302158535 -0.574143153586594 1.74646076035339 1.75438767612502 1.74380874666379 -1.13287411273457 -0.795433018475884 -0.712970858283911 +TR5075|c0_g1_i1 -1.04544737992556 -0.329240345926152 -0.393370683345868 2.50474970263492 2.07793503557972 2.30706903479522 -2.04544737992556 -1.68287730054085 -1.39337068334587 +TR131|c0_g1_i1 -3.50802026981862 -3.6944333940495 -3.55241438917708 1.98577454287534 1.99158406095747 1.95736061514986 1.41625240401813 1.71671228997234 1.68718414007205
--- /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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 +TR2107|c1_g1_i1 2.49178842221691 2.62929194596684 2.16986032732955 -1.41510217339161 -2.41510217339161 -1.83013967267045 -0.607747251334006 -0.607747251334006 -0.41510217339161 +TR4761|c0_g1_i1 2.06406810079911 1.80544476674762 1.90822498634624 -0.339510283104669 -0.357888812419525 -0.296334141902888 -1.67981690730689 -1.51400801433681 -1.59017969482221 +TR5055|c0_g2_i1 1.90528891290538 0.865760548718745 1.50319046933404 -0.982236357836205 -0.982236357836205 0.280798047997588 -0.982236357836205 -0.304164452723568 -1.30416445272357 +TR2672|c0_g1_i1 0.965440325233136 1.96544032523314 1.58211168568163 0.965440325233136 -0.619522175488021 0.0585497296246169 -2.94145027037538 -0.619522175488021 -1.35648776965423 +TR4277|c0_g1_i1 3.24415794782388 3.31812623217364 3.18414689752048 -1.44630436384266 -1.5322044372483 -1.46308007659348 -1.98611482817144 -1.80411699442855 -1.51461037723356 +TR127|c1_g1_i1 1.25755965737847 2.52059406321227 2.02309440374145 -0.0643684375088904 -1.06436843750889 -1.06436843750889 -0.479405936787734 -2.06436843750889 -1.06436843750889 +TR1894|c2_g1_i1 2.11263053903627 1.56008951600749 1.23816142112012 -1.34680107960103 -0.346801079601032 -1.34680107960103 -1.34680107960103 -0.761838578879876 0.238161421120124
--- /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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 0.121615845393921 37.6317321909836 0 0 +TR131|c0_g1_i1 wt_37 wt_GSNO 26.1866396538608 1340.30918254958 683.247911101723 -5.68565819121436 0.188173369545145 -30.214999098745 1.5048769682518e-200 2.48304699761546e-199 +TR4761|c0_g1_i1 wt_37 wt_GSNO 1645.20640957447 193.196157329029 919.201283451752 3.09227622940716 0.143766888218033 21.5089598706309 1.28350063534336e-102 1.41185069887769e-101 +TR3091|c0_g1_i1 wt_37 wt_GSNO 16.7444693227929 328.569936894811 172.657203108802 -4.30529554105297 0.242003292489129 -17.790235400398 8.41257542126328e-71 6.94037472254221e-70 +TR3638|c0_g1_i1 wt_37 wt_GSNO 583.00358519031 183.754416330029 383.37900076017 1.66225356244238 0.144704273829591 11.4872458045013 1.52909526923641e-30 1.00920287769603e-29 +TR2487|c0_g1_i1 wt_37 wt_GSNO 342.210853400436 920.407318992504 631.30908619647 -1.42823125318502 0.124766100464834 -11.4472701147503 2.42667678802884e-30 1.33467223341586e-29 +TR3788|c0_g1_i1 wt_37 wt_GSNO 19.5075441237117 134.95369713876 77.2306206312357 -2.78185518936858 0.264520576183151 -10.5165928091826 7.24461724546331e-26 3.41531955857556e-25 +TR1479|c0_g1_i1 wt_37 wt_GSNO 129.593534475689 371.064629188207 250.329081831948 -1.5163204099518 0.145721574162894 -10.4055999851936 2.33778717306381e-25 9.6433720888882e-25 +TR2107|c1_g1_i1 wt_37 wt_GSNO 48.9228907410258 7.40521775805688 28.1640542495414 2.72565745131165 0.439033221898883 6.20831708252687 5.35550100392651e-10 1.96368370143972e-09 +TR3854|c0_g1_i1 wt_37 wt_GSNO 1573.69549271337 2374.56159860719 1974.12854566028 -0.593952181868431 0.11125243839418 -5.33877900063628 9.3574622694111e-08 3.08796254890566e-07 +TR2122|c0_g2_i2 wt_37 wt_GSNO 119.534640490118 199.143666337033 159.339153413576 -0.739897366210811 0.168946597067543 -4.37947481070013 1.18965671308372e-05 3.56897013925116e-05 +TR1449|c0_g1_i1 wt_37 wt_GSNO 180.814952011467 104.755290736358 142.785121373912 0.785811747593426 0.186397685526415 4.21578060572037 2.48915666101586e-05 6.68826557791634e-05 +TR4163|c0_g1_i1 wt_37 wt_GSNO 347.283468916919 232.772947466212 290.028208191566 0.577390309281198 0.137377906430928 4.20293425836637 2.63477128827007e-05 6.68826557791634e-05 +TR2672|c0_g1_i1 wt_37 wt_GSNO 18.3155337236093 2.26581902751323 10.2906763755613 2.9857084616452 0.76120938504973 3.92232218924907 8.76996107235725e-05 0.000206720510991278 +TR5055|c0_g2_i1 wt_37 wt_GSNO 23.3590211688541 5.52768338415684 14.4433522765055 2.08513896568298 0.577312677901881 3.61180179389265 0.000304076942398887 0.000668969273277552 +TR2844|c0_g1_i1 wt_37 wt_GSNO 158.206282615139 231.762548186068 194.984415400603 -0.551426184671918 0.155135532159314 -3.55448024702451 0.000378726959348502 0.000781124353656284 +TR127|c1_g1_i1 wt_37 wt_GSNO 13.461799216177 1.21881296083961 7.34030608850831 3.52517488060096 1.00261297574214 3.51598769005718 0.000438121297287318 0.000850470753557735 +TR5212|c0_g1_i1 wt_37 wt_GSNO 65.7079302129484 107.875371765755 86.7916509893515 -0.715754705745063 0.210644233010843 -3.39793164766215 0.000678973819799395 0.00124478533629889 +TR1894|c2_g1_i1 wt_37 wt_GSNO 13.3497721959996 2.96749216411516 8.15863218005739 2.116499695166 0.744618031030184 2.84239651333424 0.00447757649596375 0.00777684338772651 +TR24|c0_g1_i1 wt_37 wt_GSNO 69.9065207344592 41.2394742844514 55.5729975094553 0.763675526543045 0.270944643994892 2.81856660933826 0.00482386011442872 0.00795936918880738 +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 -0.403209397282847 0.189507562454757 -2.12766916559918 0.0333645231630914 0.0500467847446371 +TR3807|c0_g1_i1 wt_37 wt_GSNO 3.48709246029019 0.350050334268211 1.9185713972792 3.04810928058763 1.5874506366217 1.92012854464212 0.054841664536056 0.0786858665082543 +TR1492|c0_g1_i2 wt_37 wt_GSNO 1640.89375005483 1435.64893261411 1538.27134133447 0.192601921423702 0.101311986688034 1.90107733270273 0.0572918841322478 0.0787763406818408 +TR4084|c0_g1_i1 wt_37 wt_GSNO 93.2264707954139 121.352438036668 107.289454416041 -0.381231151484283 0.213992488133209 -1.78151651401413 0.0748281095286238 0.0987731045777834 +TR1891|c0_g1_i1 wt_37 wt_GSNO 107.628573623499 135.399287466928 121.513930545214 -0.329513668205707 0.189733845104182 -1.73671528147639 0.0824374390602302 0.104632134191831 +TR1837|c2_g1_i1 wt_37 wt_GSNO 0.308903905435236 2.22601224010275 1.26745807276899 -2.87715913917267 1.7927876855897 -1.60485213184978 0.108526350064413 1 +TR5075|c0_g1_i1 wt_37 wt_GSNO 15.8633018853512 9.23822794034992 12.5507649128506 0.776103293030194 0.516446682273216 1.5027752518693 0.132897009805761 0.160709374365211 +TR4859|c0_g1_i1 wt_37 wt_GSNO 7.32690480813971 3.17910584569163 5.25300532691567 1.23041974278822 0.82607009598701 1.48948587869905 0.136359469158361 0.160709374365211 +TR939|c0_g1_i1 wt_37 wt_GSNO 84.2568220960088 96.9171174594069 90.5869697777078 -0.203187486812456 0.203052234052516 -1.00066609835922 0.316988262617012 0.35413945679411 +TR2278|c0_g1_i1 wt_37 wt_GSNO 486.5272515724 448.140178813055 467.333715192727 0.118924512672213 0.120068895863495 0.990468945491242 0.321944960721918 0.35413945679411 +TR2011|c5_g1_i1 wt_37 wt_GSNO 5.60408627995835 7.88255079488408 6.74331853742122 -0.503428737020628 0.712267625142964 -0.70679716338305 0.479692537619297 0.510640443272154 +TR2182|c3_g2_i6 wt_37 wt_GSNO 2.24974854180929 1.3031439398571 1.77644624083319 0.878491642458711 1.45214866443311 0.604959852923636 0.545205672528742 0.562243349795265 +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 0.1895893943505 1.67633508161709 0.113097552171736 0.909953215626095 1 +TR1982|c2_g1_i1 wt_37 wt_GSNO 5.73684100209948 5.71221669652109 5.72452884931028 -0.0104554076697489 0.738553450989728 -0.0141566025529198 0.988705042660126 0.988705042660126
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf has changed
--- /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 Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /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 Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,4 @@ +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 +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
--- /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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 +TR1678|c0_g1_i1 1 1 0 0 2 0 +TR3249|c0_g1_i1 1 1 2 1 0 4 +TR1479|c0_g1_i1 141 136 178 324 354 277
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,38 @@ +sampleA sampleB logFC logCPM PValue FDR +TR131|c0_g1_i1 wt_37 wt_GSNO -5.83642810105669 16.0393552039823 0 0 +TR4277|c0_g1_i1 wt_37 wt_GSNO 4.41398153332839 17.4536476715771 1.21637348346174e-303 2.25029094440421e-302 +TR3091|c0_g1_i1 wt_37 wt_GSNO -4.45237397999856 14.0403314476332 9.11341318887913e-90 1.12398762662843e-88 +TR4761|c0_g1_i1 wt_37 wt_GSNO 2.92554296928641 16.3361450450387 3.69873891948914e-76 3.42133350052745e-75 +TR2487|c0_g1_i1 wt_37 wt_GSNO -1.58730581845079 15.8893922467915 5.42826219868508e-69 4.01691402702696e-68 +TR3854|c0_g1_i1 wt_37 wt_GSNO -0.756824867554791 17.5153344325941 9.93801411860139e-30 6.12844203980419e-29 +TR1479|c0_g1_i1 wt_37 wt_GSNO -1.67125620463691 14.56103285356 1.52685095059931e-26 8.07049788173923e-26 +TR3788|c0_g1_i1 wt_37 wt_GSNO -2.92384493547476 12.8707566447513 2.80716974025173e-26 1.29831600486643e-25 +TR3638|c0_g1_i1 wt_37 wt_GSNO 1.50400807132974 15.1071935803349 1.01131038761579e-25 4.15760937130936e-25 +TR2107|c1_g1_i1 wt_37 wt_GSNO 2.54917839024164 11.4899163098162 1.29813298421564e-11 4.80309204159787e-11 +TR2122|c0_g2_i2 wt_37 wt_GSNO -0.904224916354351 13.8984660083514 5.12805835511887e-07 1.72489235581271e-06 +TR2672|c0_g1_i1 wt_37 wt_GSNO 2.7835273976316 10.2430082688313 1.09649323769354e-05 3.26428239781416e-05 +TR2844|c0_g1_i1 wt_37 wt_GSNO -0.705628684062878 14.1849718403614 1.14691003166444e-05 3.26428239781416e-05 +TR127|c1_g1_i1 wt_37 wt_GSNO 3.25921752655672 9.85805490683478 4.65148368806407e-05 0.000122932068898836 +TR5212|c0_g1_i1 wt_37 wt_GSNO -0.868846907645273 13.0312970321941 8.02549473297866e-05 0.000197962203413474 +TR4669|c0_g2_i1 wt_37 wt_GSNO -10.5376618403783 13.0208222595793 0.000100983795793505 0.000233525027772479 +TR4163|c0_g1_i1 wt_37 wt_GSNO 0.419885302419972 14.7306501662725 0.000212062001530818 0.000461546709214134 +TR5055|c0_g2_i1 wt_37 wt_GSNO 1.89467947607274 10.6064557750525 0.000354706720299247 0.000729119369504007 +TR1894|c2_g1_i1 wt_37 wt_GSNO 1.89765713767963 9.93882107563394 0.00173125775949168 0.00337139668953643 +TR1449|c0_g1_i1 wt_37 wt_GSNO 0.634078352010786 13.7169577495829 0.00217137808425439 0.00401704945587062 +TR2779|c0_g1_i1 wt_37 wt_GSNO -0.57033686484928 14.0677674303448 0.0111989371149329 0.0197314606310723 +TR1891|c0_g1_i1 wt_37 wt_GSNO -0.481534755723158 13.501506224993 0.0143918226007056 0.0242044289193685 +TR3807|c0_g1_i1 wt_37 wt_GSNO 2.66618717222413 8.56454952883374 0.0190046641424073 0.0305727205769162 +TR24|c0_g1_i1 wt_37 wt_GSNO 0.595098414993735 12.3882263577198 0.0313658793311069 0.0483557306354564 +TR939|c0_g1_i1 wt_37 wt_GSNO -0.361675208475799 13.0833927791152 0.0549150321214498 0.0812742475397457 +TR4084|c0_g1_i1 wt_37 wt_GSNO -0.528091154047526 13.333398560375 0.0670751762392915 0.0954531354174533 +TR1837|c2_g1_i1 wt_37 wt_GSNO -2.70993930289112 8.19725290476621 0.0887918514630023 0.121677722375225 +TR5075|c0_g1_i1 wt_37 wt_GSNO 0.614944173796075 10.4357920601168 0.162306513000849 0.214476463608265 +TR4859|c0_g1_i1 wt_37 wt_GSNO 1.05953644928152 9.44251782921817 0.174748084396246 0.222954452505555 +TR2011|c5_g1_i1 wt_37 wt_GSNO -0.669059646383004 9.63015201113972 0.264703411652408 0.32646754103797 +TR1492|c0_g1_i2 wt_37 wt_GSNO 0.031711320644402 17.1368189355291 0.451877741421955 0.539337949439108 +TR3249|c0_g1_i1 wt_37 wt_GSNO -0.891916586965799 8.33958255206055 0.564868681268914 0.653129412717181 +TR2278|c0_g1_i1 wt_37 wt_GSNO -0.0377499361453361 15.4258150009092 0.736032464572516 0.825248520884336 +TR2182|c3_g2_i6 wt_37 wt_GSNO 0.715543556453753 8.45775004801063 0.789411909605702 0.859065901629735 +TR1982|c2_g1_i1 wt_37 wt_GSNO -0.179857779984199 9.4946775424438 0.881459062505158 0.931828151791167 +TR1678|c0_g1_i1 wt_37 wt_GSNO -0.501309819317686 7.93769570375269 1 1 +TR1122|c0_g1_i1 wt_37 wt_GSNO 0.0611166350434577 8.2620697940663 1 1
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf has changed
--- /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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 +TR1678|c0_g1_i1 1 1 0 0 2 0 +TR3249|c0_g1_i1 1 1 2 1 0 4 +TR1479|c0_g1_i1 141 136 178 324 354 277
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,38 @@ +sampleA sampleB logFC logCPM PValue FDR +TR131|c0_g1_i1 wt_37 wt_GSNO -5.82360148900389 16.1142242655408 6.54502972918681e-10 2.42166099979912e-08 +TR4277|c0_g1_i1 wt_37 wt_GSNO 4.41183386172098 17.3836256000268 1.71025449213644e-09 3.1639708104524e-08 +TR3091|c0_g1_i1 wt_37 wt_GSNO -4.43700179801175 14.1203688767724 4.42033048679932e-08 5.45174093371916e-07 +TR2487|c0_g1_i1 wt_37 wt_GSNO -1.58598083708684 15.9280757073272 7.01720228399587e-08 6.49091211269618e-07 +TR4761|c0_g1_i1 wt_37 wt_GSNO 2.92043321768345 16.2716301848411 5.72725934421077e-07 4.23817191471597e-06 +TR1479|c0_g1_i1 wt_37 wt_GSNO -1.67738254434994 14.6016057367881 1.03919750932434e-06 5.86155431501655e-06 +TR3638|c0_g1_i1 wt_37 wt_GSNO 1.50288215872986 15.0600281889274 1.12469315856861e-06 5.86155431501655e-06 +TR3788|c0_g1_i1 wt_37 wt_GSNO -2.93907650045598 12.9393872783943 2.35975448958161e-06 9.7012129016133e-06 +TR3854|c0_g1_i1 wt_37 wt_GSNO -0.759397690410033 17.5353083640786 1.26736309513871e-06 5.86155431501655e-06 +TR2107|c1_g1_i1 wt_37 wt_GSNO 2.46233758474327 11.260249244859 0.000163907571391064 0.000551325467406306 +TR2122|c0_g2_i2 wt_37 wt_GSNO -0.898543060702644 13.9151768182402 0.000124408949544541 0.000460313113314803 +TR2844|c0_g1_i1 wt_37 wt_GSNO -0.712202725875737 14.1973066750225 0.000243984033514541 0.000752284103336501 +TR5212|c0_g1_i1 wt_37 wt_GSNO -0.877018509573372 13.0391017777502 0.000473838954429683 0.00134861856260756 +TR4163|c0_g1_i1 wt_37 wt_GSNO 0.417694804483346 14.7107025605232 0.000805848497363675 0.00212974245731828 +TR2672|c0_g1_i1 wt_37 wt_GSNO 2.90562993555483 9.81450205355949 0.0082274827990601 0.0169120479758458 +TR1449|c0_g1_i1 wt_37 wt_GSNO 0.640011354440497 13.6755402195434 0.00227354555819906 0.00560807904355767 +TR127|c1_g1_i1 wt_37 wt_GSNO 3.09466453837236 9.33233275488244 0.00997545255499306 0.0184545872267372 +TR1894|c2_g1_i1 wt_37 wt_GSNO 1.82732320483219 9.47625819175118 0.0170307015491221 0.0286425435144326 +TR5055|c0_g2_i1 wt_37 wt_GSNO 1.79897959483123 10.2910629958573 0.0144290410083874 0.0254225960623969 +TR939|c0_g1_i1 wt_37 wt_GSNO -0.363394684962811 13.0708604932728 0.00579686595094751 0.0134052525115661 +TR1837|c2_g1_i1 wt_37 wt_GSNO -2.21418127698954 7.02378849272624 0.0306005987832277 0.0471759231241427 +TR1891|c0_g1_i1 wt_37 wt_GSNO -0.477062796219235 13.500309435849 0.00675073796972539 0.0146927826399906 +TR3807|c0_g1_i1 wt_37 wt_GSNO 1.91879773659378 7.35599058475032 0.0402625583382779 0.0572967176352417 +TR2779|c0_g1_i1 wt_37 wt_GSNO -0.600036558858356 14.0748557225205 0.0099199826931416 0.0184545872267372 +TR24|c0_g1_i1 wt_37 wt_GSNO 0.588796779058576 12.310400953631 0.0185008090691582 0.0297621711112545 +TR4859|c0_g1_i1 wt_37 wt_GSNO 1.06036244689069 8.9138577436531 0.104550838513831 0.143273371296732 +TR4084|c0_g1_i1 wt_37 wt_GSNO -0.567278869966665 13.330468891507 0.03722342192143 0.0550906644437164 +TR2011|c5_g1_i1 wt_37 wt_GSNO -0.78957797806666 9.33004998835934 0.161975973261362 0.206659000367945 +TR2182|c3_g2_i6 wt_37 wt_GSNO 1.02218394394404 7.37517597546907 0.329234058043314 0.406055338253421 +TR5075|c0_g1_i1 wt_37 wt_GSNO 0.549449880041589 10.1791103984097 0.127566698813275 0.168570280574685 +TR4669|c0_g2_i1 wt_37 wt_GSNO -6.27345157840299 13.126293325041 0.42301701782253 0.4891134268573 +TR1678|c0_g1_i1 wt_37 wt_GSNO -0.330222398445961 5.95523974949609 0.735881722270124 0.798290940778181 +TR1122|c0_g1_i1 wt_37 wt_GSNO 0.193564460109423 7.01613737702005 0.875819231521417 0.875819231521417 +TR3249|c0_g1_i1 wt_37 wt_GSNO -0.276543877903423 7.32180296800742 0.776715509946338 0.798290940778181 +TR1982|c2_g1_i1 wt_37 wt_GSNO -0.131251756802266 9.08566155151058 0.763275890632564 0.798290940778181 +TR2278|c0_g1_i1 wt_37 wt_GSNO -0.0407242590322026 15.424279874284 0.616230913043476 0.690925569169958 +TR1492|c0_g1_i2 wt_37 wt_GSNO 0.0323916193660987 17.1363857315734 0.39613877470302 0.472810795613282
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf has changed
--- /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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 +TR1678|c0_g1_i1 1 1 0 0 2 0 +TR3249|c0_g1_i1 1 1 2 1 0 4 +TR1479|c0_g1_i1 141 136 178 324 354 277
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,39 @@ +sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj +TR4277|c0_g1_i1 wt_37 wt_ph8 4705.34614971641 162.902721493704 2434.12443560506 4.85332629705957 0.130960775627329 37.0593887659196 1.26787233139334e-300 4.81791485929468e-299 +TR131|c0_g1_i1 wt_37 wt_ph8 32.0461070493257 1436.30905989883 734.177583474076 -5.49708942597102 0.198466854292742 -27.6977707212647 7.42748041554821e-169 1.41122127895416e-167 +TR3091|c0_g1_i1 wt_37 wt_ph8 20.4914097091341 321.651020117047 171.071214913091 -3.98630633515117 0.247421953542881 -16.1113687693049 2.12272588309764e-58 2.47056970915936e-57 +TR4761|c0_g1_i1 wt_37 wt_ph8 2012.6141923276 384.620292965437 1198.61724264652 2.38765562387381 0.148312557773368 16.0988095662291 2.60059969385195e-58 2.47056970915936e-57 +TR5075|c0_g1_i1 wt_37 wt_ph8 19.3833722195684 136.98672801182 78.1850501156942 -2.81556781738656 0.271397918695417 -10.3743161735385 3.2452744609063e-25 2.46640859028879e-24 +TR2779|c0_g1_i1 wt_37 wt_ph8 191.51955185349 1058.15934185376 624.839446853626 -2.46872482043468 0.248047686960726 -9.95262181511715 2.45625242439164e-23 1.55562653544804e-22 +TR1891|c0_g1_i1 wt_37 wt_ph8 131.416087212132 376.595292171713 254.005689691923 -1.51763504949468 0.163833329626194 -9.26328637132227 1.98234808918918e-20 1.07613181984555e-19 +TR1492|c0_g1_i2 wt_37 wt_ph8 2006.11782336441 890.823502721036 1448.47066304272 1.17138763330801 0.127405972315828 9.1941344037173 3.78025797563516e-20 1.7956225384267e-19 +TR2487|c0_g1_i1 wt_37 wt_ph8 418.818667162757 965.862817209246 692.340742186001 -1.2068861494209 0.138672539999103 -8.70313725722991 3.22833072204724e-18 1.36307297153106e-17 +TR3638|c0_g1_i1 wt_37 wt_ph8 713.131183384274 326.063958913919 519.597571149096 1.12959116050603 0.141514345090043 7.98216717737901 1.43786102301281e-15 5.46387188744868e-15 +TR2122|c0_g2_i2 wt_37 wt_ph8 146.135958637131 360.821667264163 253.478812950647 -1.30611123021679 0.169971549866391 -7.68429323168191 1.53843927144259e-14 5.31460839225623e-14 +TR2107|c1_g1_i1 wt_37 wt_ph8 59.5986596731862 1.89840873462066 30.7485342039034 4.94663101068376 0.648801734442532 7.62425676148051 2.45444399374e-14 7.77240598017667e-14 +TR1479|c0_g1_i1 wt_37 wt_ph8 158.005105094407 334.827472148091 246.416288621249 -1.08064044509537 0.165852688009601 -6.51566434083244 7.23686413447896e-11 2.11539105469385e-10 +TR24|c0_g1_i1 wt_37 wt_ph8 85.6614643869141 199.923709280262 142.792586833588 -1.2309601921531 0.197065470330034 -6.24645296860764 4.19878369504523e-10 1.1396698600837e-09 +TR4163|c0_g1_i1 wt_37 wt_ph8 424.593720981574 227.471218917767 326.03246994967 0.902378343080325 0.156120482680009 5.7800125107855 7.46950706225728e-09 1.89227512243851e-08 +TR1449|c0_g1_i1 wt_37 wt_ph8 220.782434528097 117.26089394399 169.021664236043 0.916182468982546 0.175267159439456 5.22734819182728 1.71958482582447e-07 4.08401396133312e-07 +TR2278|c0_g1_i1 wt_37 wt_ph8 594.657329919233 348.341653317169 471.499491618201 0.773725482804612 0.158144801146882 4.8925129197639 9.95565784679224e-07 2.22538234222415e-06 +TR5055|c0_g2_i1 wt_37 wt_ph8 28.6665933385886 6.05959103586122 17.3630921872249 2.22056293047174 0.515653625436262 4.30630722045843 1.66002467176799e-05 3.50449652928799e-05 +TR127|c1_g1_i1 wt_37 wt_ph8 16.3791628279609 1.58772512712498 8.98344397754296 3.35782864860774 0.805715621214412 4.16751091848842 3.0794376698456e-05 6.15887533969119e-05 +TR1894|c2_g1_i1 wt_37 wt_ph8 16.2826445742552 1.67571344127509 8.97917900776516 3.31835899440704 0.806156235895962 4.1162728099709 3.85048512190321e-05 7.31592173161609e-05 +TR2672|c0_g1_i1 wt_37 wt_ph8 22.3129914439134 7.89947501226409 15.1062332280887 1.4879160019133 0.490304786216721 3.03467566244728 0.00240794483755522 0.00435723351557611 +TR4084|c0_g1_i1 wt_37 wt_ph8 113.2594381118 173.837287636503 143.548362874151 -0.610546095515353 0.203809508378262 -2.99567032163291 0.0027384232210324 0.0047300037454196 +TR4859|c0_g1_i1 wt_37 wt_ph8 8.91205730249659 1.28188505334354 5.09697117792006 2.79846628921536 0.94330374949058 2.96666507551426 0.00301048704228199 0.00497384815681373 +TR1678|c0_g1_i1 wt_37 wt_ph8 0.738899982352077 7.85275634721875 4.29582816478541 -3.47431884008145 1.21198503063676 -2.8666351087324 0.00414861034620891 0.00656863304816411 +TR3807|c0_g1_i1 wt_37 wt_ph8 4.23896204531587 0.352255997713617 2.29560902151474 3.60257127355045 1.494771199452 2.41011552461755 0.0159474699414716 0.0242401543110368 +TR1859|c3_g1_i1 wt_37 wt_ph8 0.361569353912422 2.25550826604853 1.30853880998047 -2.58650633406891 1.68391965639604 -1.53600340980911 0.124537544060973 0.181135380859874 +TR3249|c0_g1_i1 wt_37 wt_ph8 1.36481976577862 4.37661229401476 2.87071602989669 -1.67837058189371 1.10474169040967 -1.51924254915312 0.128701454821489 0.181135380859874 +TR2090|c0_g1_i1 wt_37 wt_ph8 0 5.87877087384675 2.93938543692337 -4.93100736412615 3.57047444665656 -1.38105101655149 0.167263275059569 0.227000159009415 +TR1982|c2_g1_i1 wt_37 wt_ph8 7.00144976454503 11.520013112092 9.26073143831853 -0.727260398375605 0.567300823658433 -1.28196605406919 0.199854554547713 0.261878381821141 +TR1837|c2_g1_i1 wt_37 wt_ph8 0.377330628439655 1.67813520813222 1.02773291828594 -2.14007669057536 1.85335822648042 -1.15470212935544 0.248212427250958 0.314402407851213 +TR5212|c0_g1_i1 wt_37 wt_ph8 80.2050001877881 94.8352723753388 87.5201362815635 -0.236625075567937 0.216144030335029 -1.09475646956875 0.273623341840839 0.335409257740383 +TR3854|c0_g1_i1 wt_37 wt_ph8 1925.26464813324 2107.16376011081 2016.21420412203 -0.130625245556186 0.130881633584188 -0.998041069468797 0.318259444082749 0.377933089848265 +TR2844|c0_g1_i1 wt_37 wt_ph8 193.030766468894 213.82243412349 203.426600296192 -0.144061748535941 0.171730922251619 -0.838880654963595 0.401536284440309 0.450271927171227 +TR1122|c0_g1_i1 wt_37 wt_ph8 1.69354093201913 0.660517838352177 1.17702938518565 1.39462173786331 1.66721495733336 0.83649785633758 0.402874882205835 0.450271927171227 +TR2011|c5_g1_i1 wt_37 wt_ph8 6.84875389533898 4.81927837273561 5.8340161340373 0.483956961494249 0.73923753588747 0.654670438120068 0.512679962329314 0.556623959100398 +TR2182|c3_g2_i6 wt_37 wt_ph8 2.76248771922916 1.94482465855284 2.353656188891 0.516404389322082 1.10366040723296 0.467901526536394 0.639855011782969 0.675402512437579 +TR3788|c0_g1_i1 wt_37 wt_ph8 23.7579432209456 26.0024682525169 24.8802057367313 -0.125340757750782 0.352879389384873 -0.35519432849074 0.72244401329073 0.741969527163452 +TR939|c0_g1_i1 wt_37 wt_ph8 103.002135647151 102.820214322362 102.911174984756 0.000973457550311695 0.195891269167832 0.00496937691223835 0.996035027203895 0.996035027203895
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
--- /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 Tue Aug 08 09:12:09 2023 +0000 @@ -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_ph8 4705.34614971641 162.902721493704 2434.12443560506 4.84804012036106 0.130783542648097 37.0691909868646 8.81406568413535e-301 3.34934495997143e-299 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_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 +TR2107|c1_g1_i1 wt_37 wt_ph8 59.5986596731862 1.89840873462066 30.7485342039034 4.82151434610286 0.613172060454942 7.86323229164347 3.74345886500564e-15 1.29319488063831e-14 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00 +TR5055|c0_g2_i1 wt_37 wt_ph8 28.6665933385886 6.05959103586122 17.3630921872249 2.18372312866756 0.505600668447204 4.31906693354301 1.5669025864333e-05 3.30790546024808e-05 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00 +TR127|c1_g1_i1 wt_37 wt_ph8 16.3791628279609 1.58772512712498 8.98344397754296 3.22742307122337 0.758365755070441 4.25576056097574 2.08339575851481e-05 4.16679151702962e-05 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 +TR1894|c2_g1_i1 wt_37 wt_ph8 16.2826445742552 1.67571344127509 8.97917900776516 3.18830464179373 0.7590595028564 4.20033558607184 2.66519649541344e-05 5.06387334128554e-05 21.00 14.00 11.00 1.00 2.00 5.00 1.00 3.00 1.00
--- /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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 +TR131|c0_g1_i1 wt_37 wt_ph8 32.0461070493257 1436.30905989883 734.177583474076 -5.48335951236111 0.197548955320184 -27.7569653733364 1.43583336471356e-169 2.72808339295576e-168 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_ph8 20.4914097091341 321.651020117047 171.071214913091 -3.97084930318667 0.245881056057371 -16.1494722971263 1.14537343838751e-58 1.45080635529084e-57 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00 +TR5075|c0_g1_i1 wt_37 wt_ph8 19.3833722195684 136.98672801182 78.1850501156942 -2.80247674171473 0.269715041166808 -10.3905096637956 2.73885623424733e-25 2.08153073802797e-24 13.00 22.00 21.00 6.00 8.00 10.00 163.00 121.00 142.00 +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
--- /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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 +TR2779|c0_g1_i1 217 186 137 1094 1086 1088 +TR127|c1_g1_i1 16 9 23 1 1 3 +TR2107|c1_g1_i1 47 59 65 1 2 3 +TR2011|c5_g1_i1 4 11 4 4 8 3 +TR4163|c0_g1_i1 425 368 422 254 212 234 +TR5055|c0_g2_i1 27 36 17 4 11 4 +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 +TR2278|c0_g1_i1 598 497 610 409 337 323 +TR4084|c0_g1_i1 86 95 148 201 158 175 +TR4761|c0_g1_i1 1875 2089 1746 389 406 394 +TR3638|c0_g1_i1 712 647 676 344 338 324 +TR2090|c0_g1_i1 0 0 0 0 9 10 +TR3854|c0_g1_i1 1864 1878 1734 2142 2155 2216 +TR131|c0_g1_i1 31 32 28 1492 1457 1486 +TR5075|c0_g1_i1 21 13 22 121 142 163 +TR2182|c3_g2_i6 4 1 3 2 3 1 +TR3788|c0_g1_i1 22 17 30 22 27 32 +TR4859|c0_g1_i1 8 6 12 1 2 1 +TR2487|c0_g1_i1 424 386 383 989 1032 963 +TR2122|c0_g2_i2 136 145 135 398 344 369 +TR4277|c0_g1_i1 4284 4466 4701 162 170 172 +TR3091|c0_g1_i1 19 22 17 343 316 333 +TR3807|c0_g1_i1 2 6 4 1 0 0 +TR1894|c2_g1_i1 11 21 14 3 1 1 +TR5212|c0_g1_i1 78 64 89 105 84 103 +TR939|c0_g1_i1 99 96 99 103 108 107 +TR1891|c0_g1_i1 124 115 138 411 384 365 +TR2672|c0_g1_i1 22 14 29 4 7 14 +TR2844|c0_g1_i1 178 166 211 245 213 199 +TR1837|c2_g1_i1 0 1 0 3 2 0 +TR1678|c0_g1_i1 1 1 0 10 6 8 +TR3249|c0_g1_i1 1 1 2 1 7 6 +TR1479|c0_g1_i1 141 136 178 363 302 367
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,39 @@ +sampleA sampleB logFC logCPM PValue FDR +TR131|c0_g1_i1 wt_37 wt_ph8 -5.84041934032622 16.0447738584896 2.64843647765193e-68 1.00640586150773e-66 +TR4277|c0_g1_i1 wt_37 wt_ph8 4.51251378503982 17.458563860849 7.87456958793119e-51 1.49616822170693e-49 +TR3091|c0_g1_i1 wt_37 wt_ph8 -4.33866462808288 13.9337820695818 2.36438873567113e-40 2.99489239851676e-39 +TR5075|c0_g1_i1 wt_37 wt_ph8 -3.18184004176717 12.8084012906916 4.32969562983877e-23 4.11321084834683e-22 +TR2779|c0_g1_i1 wt_37 wt_ph8 -2.76000097034818 15.7797193517192 7.02929665566158e-23 5.3422654583028e-22 +TR2107|c1_g1_i1 wt_37 wt_ph8 4.48695752844007 11.251039090086 2.85694633276303e-20 1.80939934408325e-19 +TR4761|c0_g1_i1 wt_37 wt_ph8 2.0579616780365 16.4916266757798 1.87157355154512e-14 1.01599707083878e-13 +TR1891|c0_g1_i1 wt_37 wt_ph8 -1.85558303182422 14.4424152648443 1.3549609315801e-11 6.43606442500547e-11 +TR2122|c0_g2_i2 wt_37 wt_ph8 -1.63829756449903 14.4300663727902 1.82580551883595e-09 7.70895663508514e-09 +TR2487|c0_g1_i1 wt_37 wt_ph8 -1.52256386898699 15.8810632159828 1.00076368146348e-08 3.80290198956123e-08 +TR24|c0_g1_i1 wt_37 wt_ph8 -1.56069263322937 13.6137525216945 2.0641918619938e-08 7.13084461416041e-08 +TR1479|c0_g1_i1 wt_37 wt_ph8 -1.43017641947686 14.3771173732228 1.25129096758536e-07 3.96242139735364e-07 +TR127|c1_g1_i1 wt_37 wt_ph8 2.89378247411933 9.73961391632741 1.77483025831263e-06 5.18796537045229e-06 +TR1894|c2_g1_i1 wt_37 wt_ph8 2.84455594181396 9.70265363738305 3.80774768997069e-06 1.03353151584919e-05 +TR2090|c0_g1_i1 wt_37 wt_ph8 -5.84865009980137 8.72712853989006 7.1017296397318e-06 1.79910484206539e-05 +TR5055|c0_g2_i1 wt_37 wt_ph8 1.82971910256975 10.5508300754678 1.05374662314498e-05 2.50264822996933e-05 +TR1678|c0_g1_i1 wt_37 wt_ph8 -3.62297933758159 9.02581162405914 1.85386281004691e-05 4.1439286342225e-05 +TR4084|c0_g1_i1 wt_37 wt_ph8 -0.989047817791601 13.5661419902701 0.000266385708775898 0.000562369829638008 +TR1492|c0_g1_i2 wt_37 wt_ph8 0.846946606328173 16.816027085378 0.00111844437365923 0.00223688874731846 +TR4859|c0_g1_i1 wt_37 wt_ph8 2.31297110196869 9.12085217163192 0.00169405620519211 0.00321870678986502 +TR3638|c0_g1_i1 wt_37 wt_ph8 0.812150684296427 15.3469750288171 0.00195862604708162 0.0035441804661477 +TR3807|c0_g1_i1 wt_37 wt_ph8 2.91885642490418 8.37863917696072 0.00889981242694952 0.0153724032829128 +TR2672|c0_g1_i1 wt_37 wt_ph8 1.09015105073495 10.4080380170218 0.0113968048117331 0.0188295036019939 +TR3249|c0_g1_i1 wt_37 wt_ph8 -2.00248923602224 8.66772464596919 0.012175839230813 0.0192784121154539 +TR1982|c2_g1_i1 wt_37 wt_ph8 -1.11692146946545 9.86122186982139 0.0254732500230551 0.0380540735981811 +TR4163|c0_g1_i1 wt_37 wt_ph8 0.585493536631111 14.6858406628863 0.0260369977250713 0.0380540735981811 +TR1449|c0_g1_i1 wt_37 wt_ph8 0.579397661518319 13.7363873307119 0.0302958377959148 0.0426385865275838 +TR5212|c0_g1_i1 wt_37 wt_ph8 -0.580254103150409 12.8600901680646 0.0404390149604427 0.054881520303458 +TR1859|c3_g1_i1 wt_37 wt_ph8 -2.66753302288967 8.08119047667972 0.0460728591095077 0.0603713326262514 +TR2844|c0_g1_i1 wt_37 wt_ph8 -0.482774572490911 14.0537407448782 0.0727694305006538 0.0921746119674948 +TR2278|c0_g1_i1 wt_37 wt_ph8 0.462415658712107 15.2205525577595 0.0767838146787893 0.0941220954127095 +TR3854|c0_g1_i1 wt_37 wt_ph8 -0.452545415035422 17.3656485551494 0.080313088818483 0.0953717929719486 +TR3788|c0_g1_i1 wt_37 wt_ph8 -0.50904223856954 11.112562271961 0.177982574706024 0.204949631479664 +TR1837|c2_g1_i1 wt_37 wt_ph8 -2.21377059210539 7.92265348832559 0.23010293924542 0.251432947894972 +TR939|c0_g1_i1 wt_37 wt_ph8 -0.340377492720978 13.0829751506545 0.231582978324316 0.251432947894972 +TR1122|c0_g1_i1 wt_37 wt_ph8 0.90037398238529 7.98418851125693 0.694931998823269 0.733539332091228 +TR2182|c3_g2_i6 wt_37 wt_ph8 0.125015386728524 8.45393207220823 0.999999999999999 1 +TR2011|c5_g1_i1 wt_37 wt_ph8 0.0588147623425484 9.27930953984144 1 1
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed
--- /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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 +TR2779|c0_g1_i1 217 186 137 1094 1086 1088 +TR127|c1_g1_i1 16 9 23 1 1 3 +TR2107|c1_g1_i1 47 59 65 1 2 3 +TR2011|c5_g1_i1 4 11 4 4 8 3 +TR4163|c0_g1_i1 425 368 422 254 212 234 +TR5055|c0_g2_i1 27 36 17 4 11 4 +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 +TR2278|c0_g1_i1 598 497 610 409 337 323 +TR4084|c0_g1_i1 86 95 148 201 158 175 +TR4761|c0_g1_i1 1875 2089 1746 389 406 394 +TR3638|c0_g1_i1 712 647 676 344 338 324 +TR2090|c0_g1_i1 0 0 0 0 9 10 +TR3854|c0_g1_i1 1864 1878 1734 2142 2155 2216 +TR131|c0_g1_i1 31 32 28 1492 1457 1486 +TR5075|c0_g1_i1 21 13 22 121 142 163 +TR2182|c3_g2_i6 4 1 3 2 3 1 +TR3788|c0_g1_i1 22 17 30 22 27 32 +TR4859|c0_g1_i1 8 6 12 1 2 1 +TR2487|c0_g1_i1 424 386 383 989 1032 963 +TR2122|c0_g2_i2 136 145 135 398 344 369 +TR4277|c0_g1_i1 4284 4466 4701 162 170 172 +TR3091|c0_g1_i1 19 22 17 343 316 333 +TR3807|c0_g1_i1 2 6 4 1 0 0 +TR1894|c2_g1_i1 11 21 14 3 1 1 +TR5212|c0_g1_i1 78 64 89 105 84 103 +TR939|c0_g1_i1 99 96 99 103 108 107 +TR1891|c0_g1_i1 124 115 138 411 384 365 +TR2672|c0_g1_i1 22 14 29 4 7 14 +TR2844|c0_g1_i1 178 166 211 245 213 199 +TR1837|c2_g1_i1 0 1 0 3 2 0 +TR1678|c0_g1_i1 1 1 0 10 6 8 +TR3249|c0_g1_i1 1 1 2 1 7 6 +TR1479|c0_g1_i1 141 136 178 363 302 367
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,39 @@ +sampleA sampleB logFC logCPM PValue FDR +TR131|c0_g1_i1 wt_37 wt_ph8 -5.89108692370307 16.0946870940125 5.83734002581822e-38 2.21818920981092e-36 +TR4277|c0_g1_i1 wt_37 wt_ph8 4.47812345668175 17.3786096664403 2.84916418820709e-34 5.41341195759347e-33 +TR3091|c0_g1_i1 wt_37 wt_ph8 -4.37454375877296 13.9751350003907 3.03684158911758e-24 3.84666601288227e-23 +TR2779|c0_g1_i1 wt_37 wt_ph8 -2.89398117484377 15.8061264352363 2.71183962208562e-19 2.57624764098134e-18 +TR5075|c0_g1_i1 wt_37 wt_ph8 -3.21512246000432 12.8334153580766 2.25968184332891e-15 1.71735820092997e-14 +TR2107|c1_g1_i1 wt_37 wt_ph8 4.32040270723487 11.0762608486921 1.80270537224084e-11 1.1417134024192e-10 +TR4761|c0_g1_i1 wt_37 wt_ph8 2.00464775189483 16.4172477083723 4.47039820077757e-11 2.42678759470782e-10 +TR1891|c0_g1_i1 wt_37 wt_ph8 -1.89490003648365 14.4620196202787 2.6019608818427e-10 1.23593141887528e-09 +TR2122|c0_g2_i2 wt_37 wt_ph8 -1.68823123696301 14.4430864744705 9.44150971333414e-09 3.98641521229664e-08 +TR24|c0_g1_i1 wt_37 wt_ph8 -1.665273448047 13.6146325155501 3.81691570216034e-08 1.45042796682093e-07 +TR2487|c0_g1_i1 wt_37 wt_ph8 -1.57111929409714 15.8914511338271 9.80135417366337e-08 3.38592235090189e-07 +TR1479|c0_g1_i1 wt_37 wt_ph8 -1.45195340320994 14.3929474544484 4.87972014978926e-07 1.54524471409993e-06 +TR1678|c0_g1_i1 wt_37 wt_ph8 -3.32711159096413 8.62991286220581 2.09660385386408e-05 6.12853434206423e-05 +TR127|c1_g1_i1 wt_37 wt_ph8 2.68488776770857 9.36026180000128 7.01712501052367e-05 0.000190464821714214 +TR1894|c2_g1_i1 wt_37 wt_ph8 2.65840371977461 9.30640094015976 8.26981533784744e-05 0.000209501988558802 +TR2090|c0_g1_i1 wt_37 wt_ph8 -3.12073361486577 8.21515298661506 0.000232532921389067 0.000552265688299035 +TR5055|c0_g2_i1 wt_37 wt_ph8 1.75449782198233 10.3047459168783 0.000592147419555542 0.00125008899683948 +TR4084|c0_g1_i1 wt_37 wt_ph8 -0.990738086664284 13.5812840323914 0.000555059638311732 0.00124072154446152 +TR4859|c0_g1_i1 wt_37 wt_ph8 2.03844841522755 8.5557148387818 0.00395651243262561 0.00791302486525122 +TR3807|c0_g1_i1 wt_37 wt_ph8 2.27805436961797 7.32408068149202 0.00589866928719915 0.0106737825196937 +TR1492|c0_g1_i2 wt_37 wt_ph8 0.802924741594956 16.7717103141256 0.00563666782754487 0.0106737825196937 +TR1859|c3_g1_i1 wt_37 wt_ph8 -2.08358066039446 6.92308482511994 0.016512222369009 0.0272810630444497 +TR3638|c0_g1_i1 wt_37 wt_ph8 0.765536214533451 15.2959378061905 0.00664915219564584 0.0114848992470246 +TR2672|c0_g1_i1 wt_37 wt_ph8 1.15555384827173 10.1973122527932 0.0181178874953214 0.0286866552009255 +TR3249|c0_g1_i1 wt_37 wt_ph8 -1.48866796495104 8.06119288435276 0.0485882100928286 0.0657581736567205 +TR1982|c2_g1_i1 wt_37 wt_ph8 -1.06368641289493 9.64628067316551 0.0416733207176469 0.0609071610488685 +TR1837|c2_g1_i1 wt_37 wt_ph8 -1.43890969571076 6.48444225997254 0.11393330230991 0.135295796493019 +TR5212|c0_g1_i1 wt_37 wt_ph8 -0.63168831011067 12.8380836623566 0.0369371606978984 0.0561444842608055 +TR4163|c0_g1_i1 wt_37 wt_ph8 0.545743678134199 14.6411189904126 0.0480591953597163 0.0657581736567205 +TR1449|c0_g1_i1 wt_37 wt_ph8 0.549932747054718 13.6939664483469 0.0501838693696025 0.0657581736567205 +TR2844|c0_g1_i1 wt_37 wt_ph8 -0.508967050135572 14.0451022220879 0.0631262591502692 0.0799599282570077 +TR3854|c0_g1_i1 wt_37 wt_ph8 -0.504473372285636 17.3527799714624 0.0818779321593284 0.100366497485628 +TR1122|c0_g1_i1 wt_37 wt_ph8 0.501746583160273 6.50836597017328 0.579206371120405 0.611384502849317 +TR3788|c0_g1_i1 wt_37 wt_ph8 -0.524753873079964 11.0311382344715 0.196342217213272 0.213171550117267 +TR2278|c0_g1_i1 wt_37 wt_ph8 0.424377145183046 15.1829447141358 0.128541258915254 0.148017207235747 +TR2182|c3_g2_i6 wt_37 wt_ph8 -0.0429471548350905 7.57134083040984 0.954463369529891 0.954463369529891 +TR939|c0_g1_i1 wt_37 wt_ph8 -0.398499350568058 13.0523653134109 0.173205070507278 0.193582137625782 +TR2011|c5_g1_i1 wt_37 wt_ph8 -0.0410416962762211 8.85697121679121 0.94542366790428 0.954463369529891
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed
--- /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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 +TR2779|c0_g1_i1 217 186 137 1094 1086 1088 +TR127|c1_g1_i1 16 9 23 1 1 3 +TR2107|c1_g1_i1 47 59 65 1 2 3 +TR2011|c5_g1_i1 4 11 4 4 8 3 +TR4163|c0_g1_i1 425 368 422 254 212 234 +TR5055|c0_g2_i1 27 36 17 4 11 4 +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 +TR2278|c0_g1_i1 598 497 610 409 337 323 +TR4084|c0_g1_i1 86 95 148 201 158 175 +TR4761|c0_g1_i1 1875 2089 1746 389 406 394 +TR3638|c0_g1_i1 712 647 676 344 338 324 +TR2090|c0_g1_i1 0 0 0 0 9 10 +TR3854|c0_g1_i1 1864 1878 1734 2142 2155 2216 +TR131|c0_g1_i1 31 32 28 1492 1457 1486 +TR5075|c0_g1_i1 21 13 22 121 142 163 +TR2182|c3_g2_i6 4 1 3 2 3 1 +TR3788|c0_g1_i1 22 17 30 22 27 32 +TR4859|c0_g1_i1 8 6 12 1 2 1 +TR2487|c0_g1_i1 424 386 383 989 1032 963 +TR2122|c0_g2_i2 136 145 135 398 344 369 +TR4277|c0_g1_i1 4284 4466 4701 162 170 172 +TR3091|c0_g1_i1 19 22 17 343 316 333 +TR3807|c0_g1_i1 2 6 4 1 0 0 +TR1894|c2_g1_i1 11 21 14 3 1 1 +TR5212|c0_g1_i1 78 64 89 105 84 103 +TR939|c0_g1_i1 99 96 99 103 108 107 +TR1891|c0_g1_i1 124 115 138 411 384 365 +TR2672|c0_g1_i1 22 14 29 4 7 14 +TR2844|c0_g1_i1 178 166 211 245 213 199 +TR1837|c2_g1_i1 0 1 0 3 2 0 +TR1678|c0_g1_i1 1 1 0 10 6 8 +TR3249|c0_g1_i1 1 1 2 1 7 6 +TR1479|c0_g1_i1 141 136 178 363 302 367
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results Tue Aug 08 09:12:09 2023 +0000 @@ -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 0.142496869452394 -16.1586318037371 9.87286349231705e-59 3.65295949215731e-57 +TR1891|c0_g1_i1 wt_GSNO wt_ph8 128.246229498835 343.028289972482 235.637259735659 -1.41742353970608 0.104322254921704 -13.586971838079 4.78470241007372e-42 8.85169945863638e-41 +TR4761|c0_g1_i1 wt_GSNO wt_ph8 184.029205648389 351.782300021135 267.905752834762 -0.941259207260895 0.0933372308442406 -10.0844989587451 6.4694390401545e-24 7.97897481619054e-23 +TR24|c0_g1_i1 wt_GSNO wt_ph8 39.3724575919554 183.288101009647 111.330279300801 -2.22846767043702 0.242443002218073 -9.19171784728418 3.86617044826114e-20 3.57620766464156e-19 +TR3638|c0_g1_i1 wt_GSNO wt_ph8 174.266398355818 297.555274221606 235.910836288712 -0.761689698593791 0.096931480326081 -7.85802193499407 3.90246977316646e-15 2.88782763214318e-14 +TR2122|c0_g2_i2 wt_GSNO wt_ph8 190.673533226329 328.707071692642 259.690302459485 -0.789061688115737 0.103094089827314 -7.65380139091815 1.95123561209759e-14 1.20326196079352e-13 +TR4669|c0_g2_i1 wt_GSNO wt_ph8 165.630009730314 0 82.8150048651569 9.98638581786287 2.40591101973569 4.15077105343653 3.31357095210528e-05 0.000175145893182708 +TR2278|c0_g1_i1 wt_GSNO wt_ph8 426.804298570637 315.99710709695 371.400702833793 0.433055347501054 0.106340324733697 4.07235306630417 4.65405596938926e-05 0.000215250088584253 +TR4084|c0_g1_i1 wt_GSNO wt_ph8 115.544575735664 157.970364768418 136.757470252041 -0.444508945050625 0.160721197310796 -2.76571449496517 0.00567982380523222 0.0233503867548436 +TR3788|c0_g1_i1 wt_GSNO wt_ph8 128.115824993653 24.010679388938 76.0632521912957 2.41599826196159 0.930388620648679 2.59676248004531 0.00941069736448111 0.0348195802485801 +TR5075|c0_g1_i1 wt_GSNO wt_ph8 8.81552188359314 126.23137395943 67.5234479215117 -3.83892667969009 1.51640337447128 -2.53159993199606 0.0113543457832674 0.0381918903618995 +TR1492|c0_g1_i2 wt_GSNO wt_ph8 1368.89238848897 813.514514376559 1091.20345143276 0.750717599362044 0.314762309207961 2.38503015577399 0.0170777214032538 0.0526563076600326 +TR1678|c0_g1_i1 wt_GSNO wt_ph8 0.695005959508731 7.10082184137838 3.89791390044355 -3.29023865439928 1.50742518175894 -2.18268786684328 0.0290588040465541 0.0827058269017309 +TR1479|c0_g1_i1 wt_GSNO wt_ph8 353.92669362375 305.546165789569 329.736429706659 0.212056310257659 0.102841330599274 2.06197556003964 0.0392100628615187 0.0987833713777822 +TR1859|c3_g1_i1 wt_GSNO wt_ph8 0 2.05957798928713 1.02978899464357 -3.32897459707671 1.62131131542191 -2.05326057087958 0.0400473127207225 0.0987833713777822 +TR2844|c0_g1_i1 wt_GSNO wt_ph8 220.566338218013 194.214843050373 207.390590634193 0.186796872895529 0.101161116569857 1.8465283819454 0.0648155222548327 0.149885895214301 +TR2107|c1_g1_i1 wt_GSNO wt_ph8 7.08292121571621 1.78415791317121 4.43353956444371 1.99039306371489 1.13345482120575 1.75604093473928 0.0790814192381375 0.172118383047711 +TR2672|c0_g1_i1 wt_GSNO wt_ph8 2.07518941673641 7.44710458698621 4.76114700186131 -1.80710364026684 1.3788176041713 -1.31061834052587 0.189986739707629 0.390528298287903 +TR4859|c0_g1_i1 wt_GSNO wt_ph8 3.10763825129944 1.1806627783491 2.14415051482427 1.36600125700608 1.24143041683139 1.1003446012646 0.271182006077686 0.528091274993389 +TR3091|c0_g1_i1 wt_GSNO wt_ph8 312.47018793986 293.531643106953 303.000915523406 0.0884824617062953 0.0884687505769775 1.00015498273942 0.317235511103473 0.572534846408031 +TR4163|c0_g1_i1 wt_GSNO wt_ph8 221.469120691076 207.118822998308 214.293971844692 0.0967338751775785 0.098273607992398 0.984332183927362 0.324952210123477 0.572534846408031 +TR1894|c2_g1_i1 wt_GSNO wt_ph8 2.85762748931802 1.47338219762144 2.16550484346973 0.974874448083218 1.21963227734242 0.799318340612854 0.424105846774756 0.713268924121181 +TR3249|c0_g1_i1 wt_GSNO wt_ph8 2.06512931203634 4.15451161800812 3.10982046502223 -1.06280923847798 1.42172379433197 -0.747549729923012 0.454731796166159 0.726065302514524 +TR5212|c0_g1_i1 wt_GSNO wt_ph8 102.736339436612 86.4452993262187 94.5908193814151 0.250307109752951 0.347207101059796 0.720915871216134 0.470961277306718 0.726065302514524 +TR1122|c0_g1_i1 wt_GSNO wt_ph8 1.29006258579706 0.5946183773076 0.942340481552333 1.01745920560277 1.75106315862354 0.581052259932512 0.561205232532948 1 +TR2011|c5_g1_i1 wt_GSNO wt_ph8 7.597917075274 4.42090354598533 6.00941031062966 0.776221433822191 1.38068634268979 0.562199689981717 0.573979972628469 0.849490359490134 +TR1837|c2_g1_i1 wt_GSNO wt_ph8 2.16507864525674 1.46465683073113 1.81486773799393 0.574055870722253 1.31330872914198 0.437106567545087 0.662034064585536 0.882648546299866 +TR1982|c2_g1_i1 wt_GSNO wt_ph8 5.5352448786851 10.687042573374 8.11114372602957 -0.9487458240786 2.34310116245464 -0.404910312572544 0.685543437736728 0.882648546299866 +TR2182|c3_g2_i6 wt_GSNO wt_ph8 1.29006258579706 1.76655578876639 1.52830918728173 -0.570835750385155 1.46441538912588 -0.389804528567465 0.69668109483689 0.882648546299866 +TR1449|c0_g1_i1 wt_GSNO wt_ph8 98.9943307118646 106.843279101242 102.918804906553 -0.106933839690289 0.276431863357607 -0.386836156987999 0.698877507680504 0.882648546299866 +TR4277|c0_g1_i1 wt_GSNO wt_ph8 153.969096204861 149.159426886469 151.564261545665 0.0465928591855008 0.127909639606227 0.364263861026722 0.715660983486378 0.882648546299866 +TR3854|c0_g1_i1 wt_GSNO wt_ph8 2260.55060252051 1927.46472630351 2094.00766441201 0.229965172704227 0.793466242289089 0.289823511635221 0.771951259799004 0.910963182508494 +TR127|c1_g1_i1 wt_GSNO wt_ph8 1.20754470361908 1.49113571265046 1.34934020813477 -0.373671738849602 1.38864714646406 -0.269090488394471 0.787860049737076 0.910963182508494 +TR2090|c0_g1_i1 wt_GSNO wt_ph8 9.46045896251181 5.6546754787973 7.55756722065455 0.740040477295999 3.75055668025179 0.19731483627287 0.843581169905129 0.945833432923932 +TR3807|c0_g1_i1 wt_GSNO wt_ph8 0.347502979754365 0.292870809896544 0.320186894825454 0.331202385322155 1.89086385045428 0.175159298350637 0.860954465054859 1 +TR131|c0_g1_i1 wt_GSNO wt_ph8 1275.67603302799 1312.2934796972 1293.9847563626 -0.0408368749216137 0.405274721880999 -0.100763439506115 0.91973825012661 0.956831887096637 +TR5055|c0_g2_i1 wt_GSNO wt_ph8 5.17791343714095 5.60171771495863 5.38981557604979 -0.113901914254778 1.2463123048958 -0.0913911495596612 0.927181793948442 0.956831887096637 +TR939|c0_g1_i1 wt_GSNO wt_ph8 92.2508462008296 94.0990807885678 93.1749634946987 -0.0286723936076184 0.345661698999674 -0.0829492931689995 0.933891858779043 0.956831887096637 +TR2487|c0_g1_i1 wt_GSNO wt_ph8 875.181494043204 882.631049341941 878.906271692572 -0.0122873741271473 0.22699904980564 -0.0541296280212096 0.956831887096637 0.956831887096637
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
--- /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 Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /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 Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 +TR3854|c0_g1_i1 2173 2151 1775 2142 2155 2216 +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 +TR3091|c0_g1_i1 308 284 250 343 316 333 +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 +TR939|c0_g1_i1 89 88 72 103 108 107 +TR1891|c0_g1_i1 139 111 97 411 384 365 +TR2672|c0_g1_i1 4 2 0 4 7 14 +TR2844|c0_g1_i1 214 223 161 245 213 199 +TR1837|c2_g1_i1 1 4 1 3 2 0 +TR1678|c0_g1_i1 0 2 0 10 6 8 +TR3249|c0_g1_i1 1 0 4 1 7 6 +TR1479|c0_g1_i1 324 354 277 363 302 367
--- /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 Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,40 @@ +sampleA sampleB logFC logCPM PValue FDR +TR2779|c0_g1_i1 wt_GSNO wt_ph8 -2.23950613357817 15.9163032020312 4.60955581344059e-235 1.79772676724183e-233 +TR1492|c0_g1_i2 wt_GSNO wt_ph8 0.807687320151986 16.8439413499966 1.06317515303199e-90 2.07319154841239e-89 +TR5075|c0_g1_i1 wt_GSNO wt_ph8 -3.74688019557381 12.8681343619696 5.1381781460234e-32 6.67963158983042e-31 +TR24|c0_g1_i1 wt_GSNO wt_ph8 -2.16553693339805 13.5635491898429 9.2971773987615e-26 9.06474796379246e-25 +TR3854|c0_g1_i1 wt_GSNO wt_ph8 0.290142827557204 17.7786481597017 1.25773893145984e-24 9.81036366538678e-24 +TR3788|c0_g1_i1 wt_GSNO wt_ph8 2.47729608121809 13.0242288909359 1.10830409992816e-22 7.20397664953306e-22 +TR1891|c0_g1_i1 wt_GSNO wt_ph8 -1.3583596459138 14.6310791041785 1.59601754746587e-15 8.89209776445273e-15 +TR4761|c0_g1_i1 wt_GSNO wt_ph8 -0.879210949997969 14.8138025433621 1.16981383272981e-13 5.70284243455784e-13 +TR2122|c0_g2_i2 wt_GSNO wt_ph8 -0.729742458144456 14.7699470890569 4.10258938208877e-06 1.77778873223847e-05 +TR3638|c0_g1_i1 wt_GSNO wt_ph8 -0.706925054082112 14.6354932126397 1.54507784026086e-05 6.02580357701737e-05 +TR4669|c0_g2_i1 wt_GSNO wt_ph8 10.4046228735587 13.1113136633968 0.000139728809507287 0.000495402142798563 +TR1678|c0_g1_i1 wt_GSNO wt_ph8 -3.01399259671531 9.36047067579877 0.000442811746352842 0.00143913817564674 +TR2278|c0_g1_i1 wt_GSNO wt_ph8 0.489116151456685 15.2921561061716 0.00123564582245084 0.00370693746735251 +TR2107|c1_g1_i1 wt_GSNO wt_ph8 1.97628703812853 9.36554809158219 0.00657205660686984 0.0183078719762803 +TR1479|c0_g1_i1 wt_GSNO wt_ph8 0.27208346223967 15.1172591193697 0.0367666005878079 0.0955931615283007 +TR1859|c3_g1_i1 wt_GSNO wt_ph8 -4.1298851005078 8.3758408307508 0.0437166707415215 0.106559384932459 +TR4084|c0_g1_i1 wt_GSNO wt_ph8 -0.387761437724876 13.8602939725323 0.0668673830079525 0.153401643371185 +TR2672|c0_g1_i1 wt_GSNO wt_ph8 -1.63593346878775 9.53972870485612 0.0715566666179246 0.155039444338837 +TR1982|c2_g1_i1 wt_GSNO wt_ph8 -0.864358765411198 10.0957379798877 0.108379561457656 0.222463310360452 +TR5212|c0_g1_i1 wt_GSNO wt_ph8 0.312770273727969 13.3365736924153 0.135331780456409 0.263896971889998 +TR2844|c0_g1_i1 wt_GSNO wt_ph8 0.241817510473408 14.4560087242059 0.15465951473335 0.287224813076222 +TR3091|c0_g1_i1 wt_GSNO wt_ph8 0.14889261782812 14.9963282436933 0.186547888961471 0.324612319602237 +TR4859|c0_g1_i1 wt_GSNO wt_ph8 1.30848594262338 8.73097118348756 0.191438034637217 0.324612319602237 +TR2011|c5_g1_i1 wt_GSNO wt_ph8 0.790825548309762 9.70516893221035 0.218107108399401 0.354424051149027 +TR4163|c0_g1_i1 wt_GSNO wt_ph8 0.155999611692108 14.5006318412937 0.284866034395977 0.444391013657724 +TR1894|c2_g1_i1 wt_GSNO wt_ph8 0.986980002958084 8.78386674332455 0.331299000761855 0.496948501142782 +TR3249|c0_g1_i1 wt_GSNO wt_ph8 -0.985518730250915 9.08501700013798 0.456425031570127 0.65928060115685 +TR4277|c0_g1_i1 wt_GSNO wt_ph8 0.105816203369183 14.0046181837143 0.523017417566317 0.728488545895941 +TR2487|c0_g1_i1 wt_GSNO wt_ph8 0.0464385825187709 16.5266539544117 0.56789954734259 0.759378620070234 +TR131|c0_g1_i1 wt_GSNO wt_ph8 0.0192051247671651 17.0827736541362 0.598052390607106 0.759378620070234 +TR1837|c2_g1_i1 wt_GSNO wt_ph8 0.590866113458774 8.6619486530175 0.603608646722493 0.759378620070234 +TR2090|c0_g1_i1 wt_GSNO wt_ph8 0.774122590048598 9.89437120476407 0.740004802646486 0.88514773566839 +TR1122|c0_g1_i1 wt_GSNO wt_ph8 0.904237754221878 8.22931948652769 0.748971160950176 0.88514773566839 +TR1449|c0_g1_i1 wt_GSNO wt_ph8 -0.0429337811569824 13.4582943043574 0.870095339425673 0.988074012458205 +TR939|c0_g1_i1 wt_GSNO wt_ph8 0.0314734152791246 13.3146965055009 0.886733088103517 0.988074012458205 +TR5055|c0_g2_i1 wt_GSNO wt_ph8 -0.0547681668951162 9.62768076070569 1 1 +TR2182|c3_g2_i6 wt_GSNO wt_ph8 -0.52401851151559 8.52973766897149 1 1 +TR127|c1_g1_i1 wt_GSNO wt_ph8 -0.306284780231878 8.45768988187045 1 1 +TR3807|c0_g1_i1 wt_GSNO wt_ph8 0.273602957097835 7.94319392916032 1 1
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed
--- /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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 +TR3854|c0_g1_i1 2173 2151 1775 2142 2155 2216 +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 +TR3091|c0_g1_i1 308 284 250 343 316 333 +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 +TR939|c0_g1_i1 89 88 72 103 108 107 +TR1891|c0_g1_i1 139 111 97 411 384 365 +TR2672|c0_g1_i1 4 2 0 4 7 14 +TR2844|c0_g1_i1 214 223 161 245 213 199 +TR1837|c2_g1_i1 1 4 1 3 2 0 +TR1678|c0_g1_i1 0 2 0 10 6 8 +TR3249|c0_g1_i1 1 0 4 1 7 6 +TR1479|c0_g1_i1 324 354 277 363 302 367
--- /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 Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,40 @@ +sampleA sampleB logFC logCPM PValue FDR +TR2779|c0_g1_i1 wt_GSNO wt_ph8 -2.23795519272236 15.9076254017254 2.92187316761747e-09 1.13953053537081e-07 +TR1492|c0_g1_i2 wt_GSNO wt_ph8 0.807554446371668 16.8426446227048 5.58321346449028e-08 1.0887266255756e-06 +TR24|c0_g1_i1 wt_GSNO wt_ph8 -2.16839334936065 13.5222768601527 3.73856822091552e-07 4.86013868719017e-06 +TR3788|c0_g1_i1 wt_GSNO wt_ph8 2.47096654484901 13.0144557887788 1.24573204904324e-06 9.71670998253725e-06 +TR5075|c0_g1_i1 wt_GSNO wt_ph8 -3.68481140303272 12.7944067233298 3.44359702134402e-06 2.23833806387361e-05 +TR3854|c0_g1_i1 wt_GSNO wt_ph8 0.290746293924475 17.7782076349597 5.253221448666e-07 5.12189091244935e-06 +TR1891|c0_g1_i1 wt_GSNO wt_ph8 -1.35768165107067 14.6117632515968 5.28666359293914e-06 2.79053243123478e-05 +TR4761|c0_g1_i1 wt_GSNO wt_ph8 -0.87892005602825 14.8002262876656 5.72416908971236e-06 2.79053243123478e-05 +TR2122|c0_g2_i2 wt_GSNO wt_ph8 -0.73016604040274 14.7551588447381 0.000213340170514584 0.000924474072229863 +TR3638|c0_g1_i1 wt_GSNO wt_ph8 -0.708321413581678 14.6195575978943 0.000258928735946679 0.00100982207019205 +TR2107|c1_g1_i1 wt_GSNO wt_ph8 1.90861736829884 8.90712643491077 0.00457979737107358 0.0148843414559891 +TR1678|c0_g1_i1 wt_GSNO wt_ph8 -2.86408187112217 8.67828416118206 0.00614682516188998 0.01844047548567 +TR2278|c0_g1_i1 wt_GSNO wt_ph8 0.503051556783975 15.2850549214884 0.00155857674629243 0.00552586300958226 +TR1859|c3_g1_i1 wt_GSNO wt_ph8 -1.96144637998691 6.77065030795652 0.0428269385052536 0.0982500353944054 +TR2672|c0_g1_i1 wt_GSNO wt_ph8 -1.69730734417424 8.97832173338033 0.0866262290356742 0.160877282494824 +TR1479|c0_g1_i1 wt_GSNO wt_ph8 0.277933522953328 15.1098597149167 0.0157877120065796 0.0439800548754716 +TR1982|c2_g1_i1 wt_GSNO wt_ph8 -0.859948395691952 9.74982883974683 0.0845253825418728 0.160877282494824 +TR4859|c0_g1_i1 wt_GSNO wt_ph8 1.04376243585308 7.84838377560073 0.178339170085145 0.28980115138836 +TR2011|c5_g1_i1 wt_GSNO wt_ph8 0.835627288758852 9.33803398810951 0.117576176969538 0.208430495536908 +TR4084|c0_g1_i1 wt_GSNO wt_ph8 -0.383433512314591 13.8345091917852 0.0320674039619627 0.0833752503011029 +TR1894|c2_g1_i1 wt_GSNO wt_ph8 0.899367664455804 7.86698528437277 0.236693956821627 0.369242572641738 +TR5212|c0_g1_i1 wt_GSNO wt_ph8 0.317453614519528 13.3093804544918 0.0408068910563263 0.0982500353944054 +TR2182|c3_g2_i6 wt_GSNO wt_ph8 -0.988859576038597 7.34392475064937 0.332144974966108 0.46263050084565 +TR3249|c0_g1_i1 wt_GSNO wt_ph8 -1.18548803762212 8.36747688877935 0.296376188714785 0.444564283072177 +TR1837|c2_g1_i1 wt_GSNO wt_ph8 0.83411458992077 7.6102620160458 0.39326030637601 0.528867308574635 +TR3807|c0_g1_i1 wt_GSNO wt_ph8 0.40219136988549 5.09566487188118 0.681998347783058 0.765740423023183 +TR4669|c0_g2_i1 wt_GSNO wt_ph8 6.05037553674292 13.1239272719772 0.480074268471177 0.603964402270191 +TR1122|c0_g1_i1 wt_GSNO wt_ph8 0.184244267394782 6.64199260311611 0.869699168726351 0.892585988955992 +TR127|c1_g1_i1 wt_GSNO wt_ph8 -0.354388761220407 7.15556768591471 0.687202943738754 0.765740423023183 +TR2844|c0_g1_i1 wt_GSNO wt_ph8 0.251980888130197 14.4425124782726 0.0594765231313182 0.128865800117856 +TR2090|c0_g1_i1 wt_GSNO wt_ph8 -0.862128177746631 9.64998833298881 0.646749723219787 0.764340581987021 +TR3091|c0_g1_i1 wt_GSNO wt_ph8 0.148831558112851 14.9878570236746 0.0841354210369898 0.160877282494824 +TR5055|c0_g2_i1 wt_GSNO wt_ph8 0.0583511298028353 9.18288041060754 0.918331019801174 0.918331019801174 +TR4163|c0_g1_i1 wt_GSNO wt_ph8 0.161834057105863 14.4879250602579 0.126768900432678 0.214955961603237 +TR4277|c0_g1_i1 wt_GSNO wt_ph8 0.103273026252208 13.9874746529507 0.308290785081446 0.445308911784311 +TR939|c0_g1_i1 wt_GSNO wt_ph8 0.0333503331526316 13.2856573711711 0.71526087918478 0.774865952450178 +TR1449|c0_g1_i1 wt_GSNO wt_ph8 -0.049884213852527 13.4293306544833 0.752342224679971 0.793009371959969 +TR2487|c0_g1_i1 wt_GSNO wt_ph8 0.0480185034754555 16.5239765307922 0.407818984620183 0.530164680006237 +TR131|c0_g1_i1 wt_GSNO wt_ph8 0.0203187870937285 17.0810493411762 0.539920494505375 0.658028102678426
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed
--- /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 Tue Aug 08 09:12:09 2023 +0000 @@ -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 +TR3854|c0_g1_i1 2173 2151 1775 2142 2155 2216 +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 +TR3091|c0_g1_i1 308 284 250 343 316 333 +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 +TR939|c0_g1_i1 89 88 72 103 108 107 +TR1891|c0_g1_i1 139 111 97 411 384 365 +TR2672|c0_g1_i1 4 2 0 4 7 14 +TR2844|c0_g1_i1 214 223 161 245 213 199 +TR1837|c2_g1_i1 1 4 1 3 2 0 +TR1678|c0_g1_i1 0 2 0 10 6 8 +TR3249|c0_g1_i1 1 0 4 1 7 6 +TR1479|c0_g1_i1 324 354 277 363 302 367
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/express_bowtie/results.xprs Tue Aug 08 09:12:09 2023 +0000 @@ -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 +2 TRINITY_DN1_c0_g1_i1 380 109.247050 5 5 5.000000 17.391774 0.000000e00 0.000000e00 4.160711e06 4.160711e06 4.160711e06 T 6.610131e+05 +3 TRINITY_DN2_c0_g1_i1 279 0.000000 0 0 0.000000 0.000000 0.000000e00 0.000000e00 0.000000e00 0.000000e00 0.000000e00 F 0.000000e+00 +4 TRINITY_DN0_c0_g1_i1 229 0.000000 0 0 0.000000 0.000000 0.000000e00 0.000000e00 0.000000e00 0.000000e00 0.000000e00 F 0.000000e+00 +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/express_bowtie/results_B.xprs Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/express_bowtie/sample_A Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/express_bowtie/sample_B Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/kallisto/abundance.tsv Tue Aug 08 09:12:09 2023 +0000 @@ -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 +TRINITY_DN3_c0_g1_i1 216 18.75 7 435814
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/kallisto/abundance.tsv.genes Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/kallisto/abundance_B.tsv Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/kallisto/abundance_B.tsv.genes Tue Aug 08 09:12:09 2023 +0000 @@ -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 +TRINITY_DN2_c2_g1 541.00 279.67 15.00 62611.60
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_express_bowtie/matrix.TMM.EXPR.matrix Tue Aug 08 09:12:09 2023 +0000 @@ -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 +TRINITY_DN2_c3_g1_i1 0 0 +TRINITY_DN0_c0_g1_i1 661013.1 661013.1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_express_bowtie/matrix.TPM.not_cross_norm Tue Aug 08 09:12:09 2023 +0000 @@ -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 +TRINITY_DN2_c3_g1_i1 0 0 +TRINITY_DN0_c0_g1_i1 661013.1 661013.1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_express_bowtie/matrix.counts.matrix Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,8 @@ + sample_A.tsv sample_B.tsv +TRINITY_DN2_c1_g1_i1 10.443691 1.000000 +TRINITY_DN1_c0_g1_i1 0.000000 0.000000 +TRINITY_DN2_c2_g1_i1 1.000000 10.443691 +TRINITY_DN2_c0_g1_i1 0.000000 0.000000 +TRINITY_DN3_c0_g1_i1 0.000000 0.000000 +TRINITY_DN2_c3_g1_i1 0.000000 0.000000 +TRINITY_DN0_c0_g1_i1 17.391774 17.391774
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie/matrix.TMM.EXPR.matrix Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie/matrix.TPM.not_cross_norm Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie/matrix.counts.matrix Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie2/matrix.TMM.EXPR.matrix Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie2/matrix.TPM.not_cross_norm Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie2/matrix.counts.matrix Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm.upper_quartile_norm.matrix Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.UpperQuartile.EXPR.matrix Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,8 @@ +sample_A sample_B +TRINITY_DN2_c0_g1 0 0 +TRINITY_DN1_c0_g1 329523.81 329523.81 +TRINITY_DN0_c0_g1 0 0 +TRINITY_DN2_c1_g1 145165.14 525311.05 +TRINITY_DN3_c0_g1 0 0 +TRINITY_DN2_c2_g1 525311.05 145165.14 +TRINITY_DN2_c3_g1 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.counts.matrix Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie_none/matrix.TPM.not_cross_norm Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/matrix_rsem_bowtie_none/matrix.counts.matrix Tue Aug 08 09:12:09 2023 +0000 @@ -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
Binary file test-data/count/qcheck/input.matrix.CPM.log2.prcomp.principal_components.pdf has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/qcheck/matrix.counts.matrix Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,41 @@ + wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR24|c0_g1_i1 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00 +TR2779|c0_g1_i1 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00 +TR127|c1_g1_i1 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 +TR2107|c1_g1_i1 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00 +TR2011|c5_g1_i1 11.00 4.00 4.00 8.00 5.00 7.00 3.00 4.00 8.00 +TR4163|c0_g1_i1 368.00 422.00 425.00 172.00 216.00 210.00 234.00 254.00 212.00 +TR5055|c0_g2_i1 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00 +TR1449|c0_g1_i1 196.00 230.00 207.00 66.00 113.00 91.00 124.00 130.00 107.00 +TR1982|c2_g1_i1 7.00 7.00 6.00 4.00 3.00 8.00 16.00 9.00 11.00 +TR1859|c3_g1_i1 0.00 0.00 1.00 0.00 0.00 0.00 1.00 2.00 4.00 +TR1492|c0_g1_i2 1895.00 1906.00 1921.00 1104.00 1263.00 1319.00 899.00 929.00 922.00 +TR1122|c0_g1_i1 2.00 3.00 0.00 3.00 0.00 0.00 1.00 1.00 0.00 +TR2278|c0_g1_i1 497.00 610.00 598.00 333.00 406.00 413.00 323.00 409.00 337.00 +TR4084|c0_g1_i1 95.00 148.00 86.00 77.00 111.00 127.00 175.00 201.00 158.00 +TR4761|c0_g1_i1 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00 +TR3638|c0_g1_i1 647.00 676.00 712.00 117.00 184.00 174.00 324.00 344.00 338.00 +TR2090|c0_g1_i1 0.00 0.00 0.00 22.00 0.00 0.02 10.33 0.00 9.09 +TR3854|c0_g1_i1 1878.00 1734.00 1864.00 1775.00 2173.00 2151.00 2216.00 2142.00 2155.00 +TR131|c0_g1_i1 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00 +TR5075|c0_g1_i1 13.00 22.00 21.00 6.00 8.00 10.00 163.00 121.00 142.00 +TR2182|c3_g2_i6 1.44 2.70 3.84 3.35 0.00 0.00 1.22 2.18 2.63 +TR3788|c0_g1_i1 17.00 30.00 22.00 91.00 132.00 125.00 32.00 22.00 27.00 +TR4859|c0_g1_i1 6.00 12.00 8.00 4.00 1.00 3.00 1.00 1.00 2.00 +TR2487|c0_g1_i1 386.00 383.00 424.00 689.00 866.00 806.00 963.00 989.00 1032.00 +TR2122|c0_g2_i2 145.00 135.00 136.00 155.00 157.00 201.00 369.00 398.00 344.00 +TR4277|c0_g1_i1 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00 +TR4669|c0_g2_i1 0.00 0.00 0.00 209.00 0.00 217.50 0.14 0.06 0.18 +TR3091|c0_g1_i1 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00 +TR2130|c1_g3_i1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 +TR3807|c0_g1_i1 6.00 4.00 2.00 0.00 0.00 1.00 0.00 1.00 0.00 +TR1894|c2_g1_i1 21.00 14.00 11.00 1.00 2.00 5.00 1.00 3.00 1.00 +TR5212|c0_g1_i1 64.00 89.00 78.00 73.00 98.00 108.00 103.00 105.00 84.00 +TR939|c0_g1_i1 96.00 99.00 99.00 72.00 89.00 88.00 107.00 103.00 108.00 +TR1891|c0_g1_i1 115.00 137.96 124.00 96.53 139.00 110.94 364.77 411.00 384.00 +TR2672|c0_g1_i1 14.00 29.00 22.00 0.00 4.00 2.00 14.00 4.00 7.00 +TR2844|c0_g1_i1 166.00 211.00 178.00 161.00 214.00 223.00 199.00 245.00 213.00 +TR1837|c2_g1_i1 1.00 0.00 0.00 1.00 1.00 4.00 0.00 3.00 2.00 +TR1678|c0_g1_i1 1.00 0.00 1.00 0.00 0.00 2.00 8.00 10.00 6.00 +TR3249|c0_g1_i1 1.00 2.00 1.00 4.00 1.00 0.00 6.00 1.00 7.00 +TR1479|c0_g1_i1 136.00 178.00 141.00 277.00 324.00 354.00 367.00 363.00 302.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie/RSEM.isoforms.results Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,8 @@ +transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct +TRINITY_DN0_c0_g1_i1 TRINITY_DN0_c0_g1 229 11.55 0.00 0.00 0.00 0.00 +TRINITY_DN1_c0_g1_i1 TRINITY_DN1_c0_g1 380 123.91 5.00 329523.81 3668378.58 100.00 +TRINITY_DN2_c0_g1_i1 TRINITY_DN2_c0_g1 279 35.45 0.00 0.00 0.00 0.00 +TRINITY_DN2_c1_g1_i1 TRINITY_DN2_c1_g1 541 281.27 5.00 145165.14 1616031.03 100.00 +TRINITY_DN2_c2_g1_i1 TRINITY_DN2_c2_g1 240 15.55 1.00 525311.05 5847953.22 100.00 +TRINITY_DN2_c3_g1_i1 TRINITY_DN2_c3_g1 202 3.45 0.00 0.00 0.00 0.00 +TRINITY_DN3_c0_g1_i1 TRINITY_DN3_c0_g1 216 6.82 0.00 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie/RSEM.isoforms_B.results Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,8 @@ +transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct +TRINITY_DN0_c0_g1_i1 TRINITY_DN0_c0_g1 229 11.55 0.00 0.00 0.00 0.00 +TRINITY_DN1_c0_g1_i1 TRINITY_DN1_c0_g1 380 123.91 5.00 329523.81 3668378.58 100.00 +TRINITY_DN2_c0_g1_i1 TRINITY_DN2_c0_g1 279 35.45 0.00 0.00 0.00 0.00 +TRINITY_DN2_c2_g1_i1 TRINITY_DN2_c2_g1 541 281.27 5.00 145165.14 1616031.03 100.00 +TRINITY_DN2_c1_g1_i1 TRINITY_DN2_c1_g1 240 15.55 1.00 525311.05 5847953.22 100.00 +TRINITY_DN2_c3_g1_i1 TRINITY_DN2_c3_g1 202 3.45 0.00 0.00 0.00 0.00 +TRINITY_DN3_c0_g1_i1 TRINITY_DN3_c0_g1 216 6.82 0.00 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie/sample_A Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,8 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 11.55 0.00 0.00 0.00 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 123.91 5.00 329523.81 3668378.58 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 35.45 0.00 0.00 0.00 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 541.00 281.27 5.00 145165.14 1616031.03 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 240.00 15.55 1.00 525311.05 5847953.22 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.45 0.00 0.00 0.00 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.82 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie/sample_B Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,8 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 11.55 0.00 0.00 0.00 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 123.91 5.00 329523.81 3668378.58 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 35.45 0.00 0.00 0.00 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 541.00 281.27 5.00 145165.14 1616031.03 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 240.00 15.55 1.00 525311.05 5847953.22 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.45 0.00 0.00 0.00 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.82 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie2/RSEM.isoforms.results Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,8 @@ +transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct +TRINITY_DN0_c0_g1_i1 TRINITY_DN0_c0_g1 229 10.58 0.00 0.00 0.00 0.00 +TRINITY_DN1_c0_g1_i1 TRINITY_DN1_c0_g1 380 122.00 5.00 309046.31 3415300.55 100.00 +TRINITY_DN2_c0_g1_i1 TRINITY_DN2_c0_g1 279 32.50 0.00 0.00 0.00 0.00 +TRINITY_DN2_c1_g1_i1 TRINITY_DN2_c1_g1 541 279.67 6.00 161779.66 1787842.67 100.00 +TRINITY_DN2_c2_g1_i1 TRINITY_DN2_c2_g1 240 14.25 1.00 529174.03 5847953.22 100.00 +TRINITY_DN2_c3_g1_i1 TRINITY_DN2_c3_g1 202 3.17 0.00 0.00 0.00 0.00 +TRINITY_DN3_c0_g1_i1 TRINITY_DN3_c0_g1 216 6.25 0.00 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie2/RSEM.isoforms_B.results Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,8 @@ +transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct +TRINITY_DN0_c0_g1_i1 TRINITY_DN0_c0_g1 380 122.00 5.00 309046.31 3415300.55 100.00 +TRINITY_DN1_c0_g1_i1 TRINITY_DN1_c0_g1 229 10.58 0.00 0.00 0.00 0.00 +TRINITY_DN2_c0_g1_i1 TRINITY_DN2_c0_g1 279 32.50 0.00 0.00 0.00 0.00 +TRINITY_DN2_c2_g1_i1 TRINITY_DN2_c2_g1 541 279.67 6.00 161779.66 1787842.67 100.00 +TRINITY_DN2_c1_g1_i1 TRINITY_DN2_c1_g1 240 14.25 1.00 529174.03 5847953.22 100.00 +TRINITY_DN2_c3_g1_i1 TRINITY_DN2_c3_g1 202 3.17 0.00 0.00 0.00 0.00 +TRINITY_DN3_c0_g1_i1 TRINITY_DN3_c0_g1 216 6.25 0.00 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie2/sample_A Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,8 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 10.58 0.00 0.00 0.00 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 122.00 5.00 309046.31 3415300.55 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 32.50 0.00 0.00 0.00 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 541.00 279.67 6.00 161779.66 1787842.67 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 240.00 14.25 1.00 529174.03 5847953.22 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.17 0.00 0.00 0.00 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.25 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie2/sample_B Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,8 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 380.00 122.00 5.00 309046.31 3415300.55 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 229.00 10.58 0.00 0.00 0.00 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 32.50 0.00 0.00 0.00 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 541.00 279.67 6.00 161779.66 1787842.67 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 240.00 14.25 1.00 529174.03 5847953.22 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.17 0.00 0.00 0.00 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.25 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/salmon/sample_A Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,8 @@ +Name Length EffectiveLength TPM NumReads +TRINITY_DN1_c0_g1_i1 380 120.403 179183 13 +TRINITY_DN0_c0_g1_i1 229 229 55271.5 7.62686 +TRINITY_DN2_c0_g1_i1 279 31.1522 565494 10.6151 +TRINITY_DN2_c1_g1_i1 541 278.129 113370 19 +TRINITY_DN2_c2_g1_i1 240 240 32900.7 4.75801 +TRINITY_DN2_c3_g1_i1 202 202 0 0 +TRINITY_DN3_c0_g1_i1 216 216 53781.8 7
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/salmon/sample_B Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/samples.txt Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/trinityStats/statsfile.txt Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,40 @@ + + +################################ +## Counts of transcripts, etc. +################################ +Total trinity 'genes': 7 +Total trinity transcripts: 7 +Percent GC: 42.12 + +######################################## +Stats based on ALL transcript contigs: +######################################## + + Contig N10: 541 + Contig N20: 541 + Contig N30: 380 + Contig N40: 380 + Contig N50: 279 + + Median contig length: 240 + Average contig: 298.14 + Total assembled bases: 2087 + + +##################################################### +## Stats based on ONLY LONGEST ISOFORM per 'GENE': +##################################################### + + Contig N10: 541 + Contig N20: 541 + Contig N30: 380 + Contig N40: 380 + Contig N50: 279 + + Median contig length: 240 + Average contig: 298.14 + Total assembled bases: 2087 + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/trinotate/genes.lengths.txt Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/trinotate/go_annotations.txt Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered/Trinity_filtered_exp.fasta Tue Aug 08 09:12:09 2023 +0000 @@ -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 max_expr_any=222.00 +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 max_expr_any=1094.00 +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 max_expr_any=65.00 +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 max_expr_any=425.00 +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 max_expr_any=36.00 +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG +CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT +ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA +TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered/Trinity_filtered_hi_iso.fasta Tue Aug 08 09:12:09 2023 +0000 @@ -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 max_expr_any= +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 max_expr_any= +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 max_expr_any= +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 max_expr_any= +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 max_expr_any= +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 max_expr_any= +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 max_expr_any= +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG +CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT +ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA +TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered/Trinity_filtered_pct_iso.fasta Tue Aug 08 09:12:09 2023 +0000 @@ -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 max_expr_any=222.00 +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 max_expr_any=1094.00 +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 max_expr_any=23.00 +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 max_expr_any=65.00 +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 max_expr_any=11.00 +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 max_expr_any=425.00 +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 max_expr_any=36.00 +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG +CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT +ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA +TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered/counts.matrix Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/norm/Trinity.fasta Tue Aug 08 09:12:09 2023 +0000 @@ -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 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/norm/Trinity_paired_unmerged_1.fasta Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/norm/Trinity_paired_unmerged_1.map Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw/Trinity.fasta Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw/Trinity_single_unmerged_1.fasta Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,2 @@ +>TRINITY_DN0_c0_g1_i1 len=226 path=[0:0-225] +CTTTACATCTGTACCATATACATATCCACCTGAAAACATTTTCTACATCCACTGTTATATGGAATGCTTGATAAGCTTTTCATTCTAACCATCAGAGCACAGTTCACAGTATGAATACATTTCCAGTAAATCTAACCTCCCAAAACCATGCCAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATCTACATCAAGCCCCGCCACCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw/Trinity_single_unmerged_1.map Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,1 @@ +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw/map.tsv Tue Aug 08 09:12:09 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.left.fq Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,400 @@ +@61DFRAAXX100204:1:100:10494:3070/1 +ACTGCATCCTGGAAAGAATCAATGGTGGCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTTT ++ +ACCCCCCCCCCCCCCCCCCCCCCCCCCCCCBC?CCCCCCCCC@@CACCCCCACCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:100:10497:13422/1 +GTAATTTCCGTACCTGCCACAGTGTGGGCTCACCCTGCTTAGAGGACAGGGAAGGACCCTAAAGGTAGGCTGATGC ++ +CCCCCCCCCCCCCCCCCCCCCCDCDCCCCCCCCCCCCCCCCCCCDDCCDDCDCBDCCDDDDBADDADDB@DBBBA@ +@61DFRAAXX100204:1:100:10546:4478/1 +CTGGGCTGCAGCTAAGTTCTCTGCATCCTCCTTCTTGCTTGTGGCTGGGAAGAAGACAATGTTGTCGATGGTCTGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC7CB@CA:>AB?C=C@@@@?A@?5:88: +@61DFRAAXX100204:1:100:10609:6818/1 +CACGTTTTCTAAGCAGTTTGTACCAGATCGTGCTAACTGCTCATTGTCTTGTTGTACACACCAGTAAAGCTGGGCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:100:10648:5988/1 +TGCTCATTGTCTTGTTGTACACACCAGTAAAGCTGGGCAAAAATATCATCCAAAAGTACATCGCTGAGAACTCCTA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCDCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:100:11486:13583/1 +CCCACCTGAAAACATTTTCTACATCCACTGTTATATGGAATGCTTGATAAGCTTTTCATTCTAACCATCAGAGCAC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBC +@61DFRAAXX100204:1:100:1176:14271/1 +TCTGAATAAGTCCTGCCACCAATGTTTTTCATAAGTGTGGCCATATGTTTTCATTATTTCAAACATTACTGTTAAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCDCDCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCDBBABDB +@61DFRAAXX100204:1:100:12152:16425/1 +CTCCGTTTTTTGAGAGTGCAACACATAGATACTGCTTGATAGCATTAATAAACATCTCATTTGTCCTGAAAACAGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:100:14680:13081/1 +GCCTGAGTGTGCAAAAATCTTCAGAGTAAGAATACCATAGTTGCTAAATATCTTTTACCATGAGCAATAATTTTTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC;CCCCCC +@61DFRAAXX100204:1:100:16086:14019/1 +TCTGGTGCAGCTAGATGGAATACTGAGAAAATGTTCTTCCATCCTGAACGAATATTTGCAGCCTGAGAATTAACCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCBCCDDCDCC +@61DFRAAXX100204:1:100:17458:1622/1 +GTGAAAGGTCATCTATTTTAATGGCTTGTCTTTAAAAACCCTAAGAGAGGGAGGATGTCACAGGGAGGGCTTGTCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCC5A############################################### +@61DFRAAXX100204:1:100:17716:21197/1 +CCAGGCTTCCCGGTGACTTTCGGATGTTAGAGTGAGGAAGTAGCTCAGCGCTTCCCTGCAGACGTTTAAAAGCCTC ++ +CCCCCCCCCCCCCBCCCCCCCCC@CCCCCC@BBCCCCCCCBDB>CCCCAC@BCBBCDDBD@?BCBA@6BBB>;A;: +@61DFRAAXX100204:1:100:19734:13092/1 +ATCATCTTGGAGACTTTTATCCACATCATGTGTTTGGGGCTCAAGATCCCCTTCATGCTCTTGGTTTATATGATCA ++ +;CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCDC +@61DFRAAXX100204:1:100:2082:1789/1 +ACGGGTGTGGTGCCAAGCATCCCTTGTTCTTGGAGGTATTGTATTCCTCTCTTTGGTTTCTTATTAAATAAATCAA ++ +CCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCADCCCDBCCCCCCCCCCDABBCCDCC@CBBBDDDD;@B?= +@61DFRAAXX100204:1:100:2172:8797/1 +GCCAAAACATAAGCAGTATCTGCACTAGCAAAAAGGGTTTGTCCTTGGTTGCACTCTAGGGATCTTGCAGCAAATT ++ +############################################################################ +@61DFRAAXX100204:1:100:2238:12815/1 +ACCATAGTTGCTAAATATCTTTTACCATGAGCAATAATTTTTTTCTCCCTTCCCCCACCCCCAATTATAAACATTT ++ +############################################################################ +@61DFRAAXX100204:1:100:2327:5980/1 +CTCCTAAATAATTTCCATCAGTGTGGGCCACCGTGATGAGTGTTTTTATTGTGTCGATATTCTTCTGTTTCATTTC ++ +CCCCCCCCCCCCCCCCCCCCCCCCC0BBBACCCBCCCCCC=CCCCCB@B@=DC@CCDDBCC-CC@CABBBB<CCCA +@61DFRAAXX100204:1:100:3665:17139/1 +ATACTTCTTTGGGTAATTTCCGTACCTGCCACAGTGTGGGCTCACCCTGCTTAGAGGACAGGGAAGGACCCTAAAG ++ +CCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCDCBCCCCCCCCCCCCCCCCCCCCCCCCBCBCDCCCBDBA>DC +@61DFRAAXX100204:1:100:6480:5393/1 +TGGAGACTTTTATCCACATCATGTGTTTGGGGCTCAAGATCCCCTTCATGCTCTTGGTTTATATGATCAACAGTCT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCBCCCCBDCBDDADBDC +@61DFRAAXX100204:1:100:8693:14085/1 +AGCTATTTCGTTATAAATGGCTGATAGATACTCTTCAGGGAGATCTTTACTGTCATTGATACCACGATTCATTTTA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:100:9306:14527/1 +GTAGAATGATGCGTGAGCTTTAAACCTGCTGTCACTGATCTTCAGAACTTTAGTGAGGAACAGTAACAGTAAGTTA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCBACDCCBCDCBCC +@61DFRAAXX100204:1:100:9656:2687/1 +CTTCTAGGCAAAGAGAGGCTACTTCAGTATCATCACAGTCTTGGAGACCCACACTGAATGCAGCCAGAAAAGGTGT ++ +BBBBBBBBBBBBBBBBBBBBB>>B>;=;=7>>?>>B>>;>BB>B################################ +@61DFRAAXX100204:1:101:11219:19264/1 +TTTGCTAACTTCTTCACTCACAGTAGAAACAGAAACCAGTGGTGCTTGCTGTCTGTTATCTGAAGATCTNGGTTGA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCABCCCCCCCCCCCCCC@CBCC;DB<>>A&>99>;@ +@61DFRAAXX100204:1:101:11349:8542/1 +GGGTAATTTCCGTACCTGCCACAGTGTGGGCTCACCCTGCTTAGAGGACAGGGAAGGACCCTAAAGGTANGCTGAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCAA;A'??@=@> +@61DFRAAXX100204:1:101:11674:10443/1 +CACCCACACCCTGTCTTCAGGTGCCACGCTCATGTCATCACTTGTGTACTCCTTGAAAGCCTGCGGTCTNTCAGAC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCACCCCCCCCCCACC&AAA?AC +@61DFRAAXX100204:1:101:1179:19106/1 +TTGGTTGAATAGAATCATGTATGTCTACAGATTTTTGTGATATTGCATCCAACGGCTTTTCACTCACAGNTGATGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@BCCCCCCCCCCCCCCCCCACCCCADCCBCA@'AA=@?? +@61DFRAAXX100204:1:101:12110:12654/1 +CTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATCCGGAAGAGAATGCGCAGCCCACACGCCAGGCNGCTTGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCBCCDCCBCCDCCDCBCDAD@ABBDDDAD@BABB.625'?A=:@0 +@61DFRAAXX100204:1:101:13165:4417/1 +CTGGATTATCAGTGCCAGACATCTGTGTACTGTAGCTGCCAATTCCTGATGATGATGTGGATTCTAAGGNGTTTAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCA?&75:;8C +@61DFRAAXX100204:1:101:13420:13159/1 +GGTGGATCCCCTCCTGTTGTCATCTTGACAGGCATCAGCCACAACAGATTCAGGGCACAGCAAGCCCTCNAAATGA ++ +CCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACAC&89848C +@61DFRAAXX100204:1:101:14810:10441/1 +CAGGAAAGAATCAATGGTGGCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTCTGNAATGCA ++ +CCCCCCCCCCCCCCCCCDCCCCCCCCCCBCBCCCBBCCCCCCCBCCCDCCCCCCCDCCDCCCDCC:A?A'AAAAAC +@61DFRAAXX100204:1:101:15025:8342/1 +GTGGGTAGGAAGCCTCTGCTGCAGGATCCTTTCACAGAGCAGAGCAATGTAAACACCAACAGAAAAACANCGGCTC ++ +CCCCCDCCCCC@CCCCCCCCCCCCCCCCCCCCCCCCCDCCCCBDBCCBCDCCCDCCDCBDACBBD=999%8====B +@61DFRAAXX100204:1:101:15551:15592/1 +CTCCCAAAACCATGCCAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATNTACATC ++ +CCCCCCCCCCCCCCCCCCCDCCCCCCCCCBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCA=7A'AAB?AC +@61DFRAAXX100204:1:101:16061:6897/1 +ATGGAATGCTTGATAAGCTTTTCATTCTAACCATCAGAGCACAGTTCACAGTATGAATACATTTCCAGTNAATCTA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCDCCCCCCCDCCCCDC=C@'ABAAAC +@61DFRAAXX100204:1:101:16516:11581/1 +GGCCCTAAAGGTAGGCTGATGCTGTGGGAACAGCCTTTCTGCTCAATATGAGCCCAACACGCGACAGAGNCCACTG ++ +74/8588857;-84;<<<<<-88;8488+8A<286A9AA##################################### +@61DFRAAXX100204:1:101:17825:1193/1 +ACGCTCATGTCATCACTTGTGTACTCCTTGAAAGCCTGCGGTCTATCAGACACATATTTTGCACAATGGNGAATAA ++ +BCCCCCCCCCCCCCCCDCCCCCCCCCCCC@CBCCCCCCC@CCCCCBCDCCCCCCCCCCCCCCCCCAABA&A>>??A +@61DFRAAXX100204:1:101:2920:3823/1 +TCCATCAGAGCACAGTTCACAGTATGAATACATTTCCAGTAAATCTAACCTCCCAAAACCATGCCAGGTNTGTTAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB'CCBC@C +@61DFRAAXX100204:1:101:4549:18278/1 +AGGTGGATCCCCTCCTGTTGTCATCTTGACAGGCATCAGCCACAACAGATTCAGGGCACAGCAAGCCCTNAAAATG ++ +AB?BA:?B<?>:>:7;=BB=??>A>>>:+>//000BBBB@B@BBBBABBBB>B@?ABBBBBB>@############ +@61DFRAAXX100204:1:101:5059:19347/1 +TTTGGACTTGCCTTTGAAGCCTGCTTTCCACAGAGCAGTCCTCTGTTCATTGTTGGAATTAAATGCTTTNGCAAAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCC&89:79C +@61DFRAAXX100204:1:101:5741:4886/1 +CCCACCCCCAATTATAAACATTTTATCCTTCAAAATACAGCTCTCCTGAGTTGTACTTCTCGCAGAAGCNCAGTCT ++ +CCCCCCBBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'B?BAAC +@61DFRAAXX100204:1:101:6207:10801/1 +GCCAAAACATAAGCAGTATCTGCACTAGCAAAAAGGGTTTGTCCTTGGTTGCACTCTAGGTATCTTGCANCAAATT ++ +DCCCCCCCDBCCCCCCCCCCCCCCCCCCCCCAC@CAA9AACCCCCCCC@CCCCCCCCCCB@CCCC########### +@61DFRAAXX100204:1:101:6228:11229/1 +CAGTGATTCAAGTTTCAGTCTGTGAAAGGTCATCTATTTTAATGGCTTTTCTTTAAAAGCCCTAAGAGANTGAGTA ++ +CBCCCCCCCCCCCCC@CCBBCC@CC@<BB@C@CC@CC?CBC?C<CCC?CCC?>>:<5?/:>A?:A########### +@61DFRAAXX100204:1:101:7284:17741/1 +CAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATCTACATCAAGCCCCGNCACCCA ++ +CCCCCCCCCCCCCCBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCC@'CCCCCC +@61DFRAAXX100204:1:101:7317:19738/1 +ATGAGAATCAATATTGTACAGAAAGTTGTACAGAATTTTTTTACATAGAAAACTTTACATCTGTACCATNTACATA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCACC'AAAAA@ +@61DFRAAXX100204:1:101:7386:20759/1 +CCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTCTGAAATGCAAGTTCTACTATGNTTTCAT ++ +CCCCCCCCCCCCCCCBBCCCCCCCCCCCBCCCCCCCDCCCCCCDCCBCCCCCCDCCBBCBCCCCCCBBC)ACBA@D +@61DFRAAXX100204:1:101:7661:3279/1 +TTGGGGCTCAAGATCCCCTTCATGCTCTTGGTTTATATGATCAACAGTCTGAGGTGGCAAATATCTAAGNTGAGGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCC'@????= +@61DFRAAXX100204:1:101:7989:14539/1 +CGTGCTCCAAGTGTGTTGCACTTGTAAAAGGTGCCTGAACATGGCTCACAGCTTCCATGAGTGCTTTAGNCGTCTT ++ +CCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCBDCCCCCCCCCABCCCCCBCCCCCCBCC=CBCCCCCCC'AA<A@C +@61DFRAAXX100204:1:101:8630:9416/1 +GAGGGAGACAGGCGAGTAGGTGGCGGTGGGGGCGAGGAGGCGTGGATGCTAGCCGCCGTCTCCGTTAGCNTCCGTC ++ +############################################################################ +@61DFRAAXX100204:1:101:9622:17436/1 +GCCAAAACATAAGCAGTATCTGCACTAGCAAAAAGGGTTTGTCCTTGGTTGCACTCTAGGTATCTTGCANCAAATT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCBBCCCBBBB'AAA=AC +@61DFRAAXX100204:1:102:10071:12692/1 +TGCGTGAGCTTTAAATTTAAAAGCCTCTGCTGGANTTCTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATCC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'CCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDBCCDCCDDAC +@61DFRAAXX100204:1:102:10556:11503/1 +TCCTGGGATTCCATTTGCTTGGATGTTTTCACTGNCACTACCATCTTCTACAGTTCCAGTGTTGCCTTCTGTACTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'BBBBBCCCCCCCCCCCCCCCCCBCBCDCDCCCDBDBCAABB +@61DFRAAXX100204:1:102:10558:14342/1 +ATGTTTTCTACCTTGGTGGATCCCCTCCTGTTGTNATCTTGACAGGCATCAGCCACAACAGATTCAGGGCACAGCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCC'CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBC +@61DFRAAXX100204:1:102:12109:19420/1 +TCTGTTATCTGAAGATCTTGGTTGAATAGAATCANGTATGTCTACAGATTTTTGTGATATTGCATCTTACCAACGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'>????DCCCCCCCCCCCCC@BACCCCCCBCDCCCDCDBDDB +@61DFRAAXX100204:1:102:12757:13134/1 +GGGATGTATTGAACCACTGCTCTCAGGACAGGAANAAACAATGCACAAGCAATTTTCTTCCTAAATAACAATTCAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC)BBBBBCCCCCCCCCCCCCCCCCC@BCCCCCCCCCCACCCCC +@61DFRAAXX100204:1:102:13549:15464/1 +GTCCATGTACATCCGGAAGAGAATGCGCAGCCCANACGCCAGGCTGCTTGTCTCCTGTTTTAGAAGATTGGGCTTG ++ +CCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCC'CCCCCCCCCCC?CCCDCCBCCCBDCDBDDBBCADA<AC@BB +@61DFRAAXX100204:1:102:13777:6235/1 +CGCAGGACTCACAAGGGTAAAGCAAATTAAGAACNCGTCTGTCTGCGGGTAGGAGAGGGGACGCAATCTGTCATAC ++ +############################################################################ +@61DFRAAXX100204:1:102:14960:18241/1 +GCCACGAATTTCCTAAATAATTTCCATCAGTGTGNGCCACCGTGATGAGTGTTTTTATTGTGTCGATATTCTTCTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC&CCCCCCCCCCCCCCDCCCCCB@BB@DCCCCDCBCCCCCCCC +@61DFRAAXX100204:1:102:15063:6971/1 +CAGAAAAGGTGTCCAAGCCAACTTAAACATCGGCNTCACGTGCTCCAAGTGTGTTGCACTTGTAAAAGGTGCCTGA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'8;9;9CCCCCCC@CBCCCCCCCCCCCCCCCCDCAACBBBBC +@61DFRAAXX100204:1:102:16420:15231/1 +GTTGTACTTCTCGCAGAAGCTCAGTCTTTACATCNATACTTCTTTGGGTAATTTCCGTACCTGCCACAGTGTGGGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCC'CCCBCCCCACCCCCCDCCCDCDDDCAB@BDBBDDCBCACCB +@61DFRAAXX100204:1:102:16908:12433/1 +CACTGATGAAATAATTCAAAAACTTTATTGACCTNTAACCTGATTAGATATGCCAGATGAGAATCAATATTGTACA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCC +@61DFRAAXX100204:1:102:17677:10400/1 +CGCACATCTTATCCCTTCTAGGCAAAGAGAGGCTNCTTCAGTATCATCACAGTCTTGGAGACCCACACTGAATGCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC',00.-;7;<4?@>:A########################## +@61DFRAAXX100204:1:102:17711:7491/1 +ACTCTGGACAATATCAAGTGGCTTTTCTTCATAGNCTCCATCATACAAGATATCATTTTTAGATAATGTTTCAGCT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCC'CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCDCCCCBCA +@61DFRAAXX100204:1:102:17798:2084/1 +CCTTGTTCTTGGAGGTTTTGTATTCCTCTCTTTGNTTTCTTATTAAATAAATCAATCCCTTGTTCTATTATTTCTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBB'BBBBBCCCCCCCCCCBBCCACCCCCCCCCCCCCCDCCCCCC +@61DFRAAXX100204:1:102:18807:10059/1 +CTGCACTGGAAATATCAGATCCGTTTTCAGGCTCNGTATCATCTTGGAGACTTTTATCCACATCATGTGTTTGGGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC&CBCCCCCCCCCC@CDCCCCCCCDCDCDC@ACDBADDBB;BA +@61DFRAAXX100204:1:102:19518:11565/1 +CCTGGGAAGAAGACAATGTTGTCGATGGTCTGGANGAGTTCCAGCTGCACAACACATTTAATCAACAGGGCAGCAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCC'BAB>BCCCBCCCCCCCDDACABCCBACCACDAD@DDBD<>C +@61DFRAAXX100204:1:102:2639:2051/1 +CTGCCTCAGAGAGTCTACTGCAAATATGGCTACANCTTCATTAGGATTACAACCAACCTTATTAAAATGATCTCCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCAA3A########################################## +@61DFRAAXX100204:1:102:3101:2926/1 +CTTCCCAGGCACTGACTCTGCTCTCGTCCATGTANATCCGGAAGAGAATGCGCAGCCCACACGCCAGGCTGCTTGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'BBBBBCCBCCCCCCCCCCCCCCCCCCC<CCCDDCAAB@B<B +@61DFRAAXX100204:1:102:5977:14503/1 +GGGGGTTCGGCCTCGCCAGAGGTGGGACGCCAAGNCAGAAGCGCGTGAGGAATTGTGGTTTTGAAGATATCCAGGG ++ +CCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCCC'CCCCCCCCCCDCACCBCBCC?CCBCCCCAACDCCCBCDCCA +@61DFRAAXX100204:1:102:6251:21399/1 +CCCAGCTATTTCGTTATAAATGGCTGATAGATACNCTTCAGGGAGATCTTTACTGTCATTGATACCACGATTCATT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'BBBBACCCCCCCCCCC@CCCDCCCCCDCDCCBCCBCDD@CC +@61DFRAAXX100204:1:102:7093:4246/1 +CGGGTCTTGTCAGCAGGGATGTTTTCTACCTTGGNGGATCCCCTCCTGTTGTCATCTTGACAGGCATCAGCCACAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC(CCCCCCCCCCB@CDCCDCCCCCCCDDDCBDDBDDBDCDABB +@61DFRAAXX100204:1:102:7907:21314/1 +AGACACATATTTTGCACAATGGCGAATAAGTCGGNTTGCTTCCATACTTGTGTCTGGGAAAGCTGCATTACATGCG ++ +>BBB>BB>BBB<B?>?>??<99:<9:A<??0000%*000089:;<74;?8BABBBBA>B################# +@61DFRAAXX100204:1:102:8037:6949/1 +TCTAGGTATCTTGCAGCAAATTTTTCCATTAATCNATCAATTTTCTGAGCTTCTCCTGGAAGCCGGAATCCTTCCA ++ +CCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCC(BBBBBCCCCCCCCCCCCCCCCCCCBCCCCCCDDDCCCCCCC +@61DFRAAXX100204:1:102:8724:1888/1 +CGGGTGTGGTGCCAAGCATCCCTTGTTCTTGGAGNTATTGTATTCCTCTCTTTGGTTTCTTATTAAATAAATCAAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBB@B&28;88DCCCCCCCCCCCCCCDCCCCCBCCDC@BCA>@BD@B +@61DFRAAXX100204:1:102:8903:16361/1 +CCTATAAGTTGTGCCAGCTCTAACTGACTGATGCNCTTCAGGATCTCATGCCACGAATTTCCTAAATAATTTCCAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC(CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:102:9691:18717/1 +ATAAGTTGTGCCAGCTCTAACTGACTGATGCACTNCAGGATCTCATGCCACGAATTTCCTAAATAATTTCCATCAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'BABBACCCCCCC;CCCCCBCCCCCCCCCCCCCCCCDCCCAC +@61DFRAAXX100204:1:103:10201:1449/1 +CTGAACACTAGAAAGGCATCCTTTTGTAAAATGTGGGAAAACTTAGCACCAGGTGAAGGTCCTGAAGAATTTCCAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCCCDCCCCCCCC?CCBCCCCCACC;CCCCCCC +@61DFRAAXX100204:1:103:11572:6697/1 +CAAAATTGAAACTAAACATTCTAACCCCTTTTTTCGCAGGCTCAATTCCTGAACATTACTCATACCGAGTTCTTGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC8CDCCCCDD +@61DFRAAXX100204:1:103:12517:20251/1 +GCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTCTGAAATGCAAGTTCTACTATGCTTTCAT ++ +CCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:13105:12342/1 +CTGGACTTCTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATCCGGAAGAGAATGCGCAGCCCACACGCCAGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCBCCCB@CCCCCB?BCCCCCCB@C@B; +@61DFRAAXX100204:1:103:13548:1359/1 +GGTGACTTTCGGATGTTAGAGTGAGGAAGAAGCTCAGCGCTTCCCTGCAGACGTTTAAAAGCCTCTGCTGGACTTC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCC+??AA?CCCCCCCCCCDCCDCBDCBCC@BBDDBDDDDBBABBACAAB +@61DFRAAXX100204:1:103:13762:1440/1 +CTCCCTTCCCCCACCCCCAATTATAAACATTTTATCCTCCAAAATACAGCTCTCCTGAGTTGTACTTCTCGCTGAA ++ +CCCCCCCCCCCCCBBBBBBCCCCCCCCCC?CCCCCCCCCCCCACCCCCCCCCCCCCCCCDCCDCCCCCCCACCBB@ +@61DFRAAXX100204:1:103:13776:4298/1 +TGATATTTGAAATACTATTCCAATTCGCAGGAAAAATCTTCTAAGAACAGCACGCAGTTCCGGAATCAAGTCAAAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDC@BCC +@61DFRAAXX100204:1:103:13798:6365/1 +GGTCACAGTCATAATTTACATAAATGTCCACCACACTCTGAGCATCTGCACAGATCCTTGTCAGTGTCTGAATAAC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCC +@61DFRAAXX100204:1:103:14748:1375/1 +CCAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATCTACATCAAGCCCCGCCACCC ++ +CCCCCCCCCCCCCCCBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@BCCCCCCCCCACCCDBD@@DDB +@61DFRAAXX100204:1:103:16156:9928/1 +CATGAGCAATAATTTTTTTCTCCCTTCCCCCACCCCCAATTATAAACATTTTATCCTTCAAAATACAGCTCTCCTG ++ +CCCCCCCCCCCCCCCCCCBBBBCCCCCCCCCC@B@BB@CCCCCCCCCACCCCCCCCCCCCAACCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:16292:7311/1 +CTGGTTCTTACATCTAATTTGCATCTATTGATGATACAAGACAACTCAAAGAGGATCGGGAACCACCCTCTCACCC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDBCDCDCCCCCCCCCCBDC +@61DFRAAXX100204:1:103:1757:15756/1 +GGCAAAAATATCATCCAAAAGTACATCGCTGAGAACTTCTAAATACTGGGTGAATACATCACATATTGCATAAAGG ++ +CCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:19512:1223/1 +CTGTTAAGCCCCTGGTTCTTACATCTAATTTGCATCTATTGATGATACAAGACAACTCAAAGAGGATCGGGAACCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCDCCDADBB@C@BB@ +@61DFRAAXX100204:1:103:2005:9846/1 +TGCTTCCCTGCAGACGTTTAAAAGCCTCTGCTGGACTTCTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCBCCCCABDBBCBBDDDC +@61DFRAAXX100204:1:103:2755:14644/1 +CTTACATCTAATTTGCATCTATTGATGATACAAGACAACTCAAAGAGGATCGGGAACCACCCTCTCACCCACACCC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC=C +@61DFRAAXX100204:1:103:3597:13520/1 +GTTGTTGTGATGTTAAAAAGCGGTACATTCCTTGGTCTTGAGTATCAACTCGAACATCGAAGTCTACTACATCTCT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCDCCCCCCCCCCCCCCCCCDCBCCCCDADDCDCDC +@61DFRAAXX100204:1:103:4062:11566/1 +GATGATACAAGACAACTCAAAGAGGATCGGGAACCACCCTCTCACCCACACCCTGTCTTCAGGTGCCACGCTCATG ++ +CCCCCCCCCCCCCBCCCCCCCCCCCCBCCCCC@CACCBCCCCCCCCCACCBCC=@BCBAC3;;-6AC@C@C?@:AB +@61DFRAAXX100204:1:103:5147:16732/1 +CATGGTTACAAGTTGTTGTCATCCATTCAGCTTTCTCTGTCTGCTGTTCTGGCAATTTCATGTTGTCAAAGATTCT ++ +CCCCCCCCCC;????CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:6646:12936/1 +GTGCAACACATAGATACTGCTTGATAGCATTAATAAACATCTCATTTGTCCTGAAAACAGGTCCTGCATTCTGCAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCDC +@61DFRAAXX100204:1:103:7220:15954/1 +GAGGAATTGTGGTTTTGAAGATATCCAGGGTGCAGTTACACGTTTTATCCCAGATTTCAAGAGTAAACTTTTCACC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCABCCCCCCCA +@61DFRAAXX100204:1:103:7253:3680/1 +CTTTACATCTGTACCATATACATATCCACCTGAAAACATTTTCTACATCCACTGTTATATGGAATGCTTGATAAGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:8055:11636/1 +TTCCTGATGATGATGTGGATTCTAAGGAGTTTAAACTTCCATATCTGTTTATAGTCTCTGGGTGTTTAACTTCACT ++ +CCCCCCCCCCCCCCCCCC<CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCBCDCCCABCCCDCC +@61DFRAAXX100204:1:103:8348:14452/1 +GTCAGAGCACAGTTCACAGTATGAATACATTTCCAGTAAATCTAACCTCCCAAAACCATGCCAGGTTTGTTATTTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDBCCDCCCDCCCBCB +@61DFRAAXX100204:1:104:12460:3347/1 +CTGATGCTGTGGGAACAGCCTTTCTGCTCAACATGAGCCCAACACGAGACAGAGGCCACTGGGTTACTAAAGGGAC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCC@CCDCDDCCCCBCCDCBB@BBAAB +@61DFRAAXX100204:1:104:12993:12947/1 +GGTGAATACATCACATATTGCATAAAGGACATGGTTACAAGTTGTTGTCATCCATTCAGCTTTCTCTGTCTGCTGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:104:13501:6860/1 +GTGATATTTGAAATACTATTCCAATTCGCAGGAAAAATCTTCTAAGAACAGCACGCAGTTCCGGAATCAAGTCAAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCBCCCCCCACCCDCBCC>A
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.right.fq Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,400 @@ +@61DFRAAXX100204:1:100:10494:3070/2 +CTCAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCATCTAGCTGC ++ +C<CCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCACCCCCACCC= +@61DFRAAXX100204:1:100:10497:13422/2 +GAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCACCC +@61DFRAAXX100204:1:100:10546:4478/2 +CTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@BCDCBCCCCCCCCCCCACCCCCCCCCBDC +@61DFRAAXX100204:1:100:10609:6818/2 +AGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGCCCTTTATGCAATATGTGATGTATTCACCCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?CBCC +@61DFRAAXX100204:1:100:10648:5988/2 +AGATGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCACCCBCCBACC +@61DFRAAXX100204:1:100:11486:13583/2 +CTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCBBBB@CCDCCCCDB@BDCCABCDDCBBCCCBC@ +@61DFRAAXX100204:1:100:1176:14271/2 +TGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCG ++ +CCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCDCCCCCCCCCC:BBBACCABC@CDDAB@DDCABDDABDBB +@61DFRAAXX100204:1:100:12152:16425/2 +CCTTTCTAGTGTTCAGGTCATTGTGTAAGCTGTCAATGAAACCACTGTCAGATGGACCACCAGATCCAAAGTCTCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCC= +@61DFRAAXX100204:1:100:14680:13081/2 +CACAGCATCAGCCTACCTTTAGGGTCCTTCCCTGTCCTCTAAGCAGGGTGAGCCCACACTGTGGCAGGGACGGGAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCDCCCCCCCCCBCCDCCB'299@'9@ +@61DFRAAXX100204:1:100:16086:14019/2 +AGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACGACCTTTTGAACATATAATGAAACGAAACAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCBCCCCCC +@61DFRAAXX100204:1:100:17458:1622/2 +AAAACATTTGGGTTGAACTTTTAGTCTTTGGGGGAGTGGTGGTCATTTTGAGGGCTTGCTGTGCCCTGAATCTGTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@CCCCCBCCCCCCCDCCCDDCBDCBB@BABA=BBDB@AB< +@61DFRAAXX100204:1:100:17716:21197/2 +GCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCAC?CCDBBCCBD@BCBBBB@B??BBA=@A?@ +@61DFRAAXX100204:1:100:19734:13092/2 +GGCTTTACTTACCGCAGTGACATCACAACACATAGAAATCCATGAAGGAACTGTGCTGCAAGCTGTGAGGACATGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCC?CC@CBCCCBCAACCC +@61DFRAAXX100204:1:100:2082:1789/2 +GGAGCAAGGATCAGTATGTGAACCCCAACTCTCAAACTACCCTTGGTCAGGAAAAACCCTCAGAGCAAGAGATACG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCBCBCCCBCDBBDACCDBCDCA@B## +@61DFRAAXX100204:1:100:2172:8797/2 +TATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAA ++ +############################################################################ +@61DFRAAXX100204:1:100:2238:12815/2 +CCCCTCCAGACCCTTTAGAAACCCAGAGGCCTCGGGCTCGCGTGTGGCTCATTTTCGCCAGAAAGGCGGTTCCCAC ++ +############################################################################ +@61DFRAAXX100204:1:100:2327:5980/2 +CAAGACTGTGATGATACTGAAGTAGCCTCTCTTTGCCTAGAAGGGATAAGATGTGCTATCAGGATTGCATGCATTT ++ +CCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCACCCC?BCCCCACBCCBCCCCCCCDDDAA@CCDBBC +@61DFRAAXX100204:1:100:3665:17139/2 +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?CCCCCC@CC@@CB@@@@DABBBCBBB +@61DFRAAXX100204:1:100:6480:5393/2 +TGCTACAATATCTATTTAGCCAGCAAAAATCTCATCAATCAGACAACAGCCAAAGCTACTCTTACTGAAATGCTGA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB +@61DFRAAXX100204:1:100:8693:14085/2 +TGCAACCAAGGACAAACCCTTTTTGCTAGTGCAGATACTGCTTATGTTTTGGCCTACTCAATTATCATGTTGACTA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:100:9306:14527/2 +GCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGCTACTTCCTCACTCTAACATCCG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCC +@61DFRAAXX100204:1:100:9656:2687/2 +TAGAAATGGAACAGATGGCCAAGACGGCTAAAGCACTCATGGAAGCTGTGAGCCATGTTCAGGCACCTTTTACAAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCD3DBBCCCDCBBCCDCBDC +@61DFRAAXX100204:1:101:11219:19264/2 +GTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@B@CBBCCCADDCCA@BC +@61DFRAAXX100204:1:101:11349:8542/2 +GTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?DDD@CDDDDDBCBBCDDDBDABB)BBBB +@61DFRAAXX100204:1:101:11674:10443/2 +CTCTGAGGCAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACG ++ +CCCCCCCCCCC@CCCCBC?CC@CBBCCC=C@CCCCAC:B@BBCC>@=@@@B>@BC@ACBB@>CBB=0;C@BBCC/? +@61DFRAAXX100204:1:101:1179:19106/2 +AAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCBCCBBCCCCACCCCACCCCCCCCCCCCCCCCBABDB>D@BDDD@ +@61DFRAAXX100204:1:101:12110:12654/2 +GCAAGCACCACTGGTTTCTGTTTCTACTGTGAGTGAAGAAGTTAGCAAAGTGAAATCCACAGCAAAATTCCCAGAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCBCDCCCCCBCCCCCDCCBCDCCBCAACCDCCAA>BBC=B<B?B +@61DFRAAXX100204:1:101:13165:4417/2 +GGACATTTATGTAAATTATGACTGTGACCTAAATGCAGCAAATATATTTGAAAGACTAGTAAATGACCTGTCGAAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCAC +@61DFRAAXX100204:1:101:13420:13159/2 +CCGGAAATCATCATCTTTCTGTGAAAATGTACAGAGATGCAGGTCTGTAATATAAAAATCTTAAACATATTGTTCC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCDCCCCCCCCC@@CCCCBCCCCCCDCDBC@ +@61DFRAAXX100204:1:101:14810:10441/2 +GGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCBCCCCCC +@61DFRAAXX100204:1:101:15025:8342/2 +GCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCDCCDCDCACCB +@61DFRAAXX100204:1:101:15551:15592/2 +GACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCCCCCCCCCDCC@ +@61DFRAAXX100204:1:101:16061:6897/2 +GGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCC +@61DFRAAXX100204:1:101:16516:11581/2 +GATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTA ++ +C@CCCCCC@CCCCBBCBBCCC=@8@CC:CCCBC?C@@CC@C@>@@CCC>C>@>A<A8@8=<??<<=:C5>BCCBCC +@61DFRAAXX100204:1:101:17825:1193/2 +AACGAAGCAGGTCTCCAACAATTCGAGATATGGTTGTACGGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCCCCCCCCCCCBCCCCCCACCCDC<ABBBA +@61DFRAAXX100204:1:101:2920:3823/2 +CAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCA ++ +CCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCBCCCCCCCCCCCDCCCCCCCACCCCCCC=C? +@61DFRAAXX100204:1:101:4549:18278/2 +GTCTGTAATATAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTA ++ +CCCCCCCCCACCCCC@@CCCBB?CCCCCCCCCCCCCCCCCCCCCCCCCCC@@@CC@=CC@@@C@@CCCCCCCCACC +@61DFRAAXX100204:1:101:5059:19347/2 +AAGAAGACAATGTTGTCGATGGTCTGGATGAGTTCCAGCTGCACAACACATTTAATCAACAGGGCAGCAAACAATT ++ +CCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCDCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCCBCDADCA?ACC +@61DFRAAXX100204:1:101:5741:4886/2 +GGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTT ++ +CCCCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCACCCCBCC:CCCCCDCDCDCBCBCBC@BCCC@?BBCBCCBD +@61DFRAAXX100204:1:101:6207:10801/2 +GGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT ++ +CCCCCACCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCBCCCCACCCCCCCCD@BCBB@BBCABC +@61DFRAAXX100204:1:101:6228:11229/2 +CTGTAATATAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTAAA ++ +CCBBCCCCCCCCC@@CCC>CCCBBC??>@BCCCCCBBCCCCC@CCCBC@@@CC@@CC@@@C@>CCCCCCCCCCC@C +@61DFRAAXX100204:1:101:7284:17741/2 +AAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTAAATACCCATAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBCCB@CCBBBCBBCCCCCCCCCBCCCCCCCCCCBA +@61DFRAAXX100204:1:101:7317:19738/2 +CATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCBCCCCCCAAC?BCCCCDCCCCCDC@ +@61DFRAAXX100204:1:101:7386:20759/2 +GATGTAGCCATATTTGCAGTAGACTCTCTGAGGCAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCD@CACBDDB@CABCCCB@BBABBAABB>>BAB>?AA>AB +@61DFRAAXX100204:1:101:7661:3279/2 +GCTGCAAGCTGTGAGGACATGCTACAATATCTATTTAGCCAGCAAAAATCTCATCAATCAGACAACAGCCAAAGCT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCD@CCC +@61DFRAAXX100204:1:101:7989:14539/2 +TGACTACAGACCTTCACAGTCCACAGGTTAAAAACAAAATGACAAAAGAACAGTACATTAAAATGAATCGTGGTAT ++ +CDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBBBCCCCCCCC?BBCCCCCCCCCC@CCCCCCC?BCCBC= +@61DFRAAXX100204:1:101:8630:9416/2 +GGCGCAGGCACCTCCACCGGCCCCGCCTTCTCTCCGCAAACGCTCCACGCACACAAAGGAGGCCCTTGAGCCTCAA ++ +############################################################################ +@61DFRAAXX100204:1:101:9622:17436/2 +ACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCACCBCCCBCCCCCCCC +@61DFRAAXX100204:1:102:10071:12692/2 +GCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACCGCTTTTTAACATCAC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCDCCCCCDCCCCDCCCCCBC +@61DFRAAXX100204:1:102:10556:11503/2 +CGGATCTGATATTTCCAGTGCAGAAAATGAACAGACAGAAGCTGATCAGGCAACTGCAGCTGAAACATTATCTAAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCDCCC +@61DFRAAXX100204:1:102:10558:14342/2 +AGAGATGCAGGTCTGTAATATAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTAT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBCCBBCCBBBCBBC +@61DFRAAXX100204:1:102:12109:19420/2 +AAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCBCCC@CCCCCCCC?CCBCCADCDCAB +@61DFRAAXX100204:1:102:12757:13134/2 +CAACGGAGCAGATTGCGTCTCACACAGAGGAACGAGAGGAAGTCTGTAACGCTCAGAGACTTGATGACAGTTCTTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCBCCCDCCCCCBCDCDCDDDDDBDCBBBDCBDBDD +@61DFRAAXX100204:1:102:13549:15464/2 +GCAAGAAGGAGGATGCAGAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCA ++ +CCCCCCCCCCCCCCCCCCBCDCCCCCCCCCBCCCCCCCCCCCCCBCCCACC@CCCCCCCBDCCC=CC?CC?CCACA +@61DFRAAXX100204:1:102:13777:6235/2 +GAAGGCCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACACGACCATGAGCCGC ++ +############################################################################ +@61DFRAAXX100204:1:102:14960:18241/2 +GCTGCATTCAGTGTGGGTCTCCAAGACTGTGATGATACTGAAGTAGCCTCTCTTTGCCTAGAAGGGATAAGATGTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCACCCCCCCCCDC +@61DFRAAXX100204:1:102:15063:6971/2 +GTATCTATCAGCCATTTATAACGAAATAGCTGGGAAAAAAATATCAATGAAAGAAACAAAAGAACTAACAATCCCT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBBCCCCCCCCCCCBBCC@BBCBBCCCCC?CCCAC +@61DFRAAXX100204:1:102:16420:15231/2 +CTACTACCCTCTCTTATGTGAAATTATGCAATTTGACTTGATTCCGGAACTGCGTGCTGTTCTTAGAAGATTTTTC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCC@CCCCCCCC>@CCCCCCCCCBC@DCBCCC +@61DFRAAXX100204:1:102:16908:12433/2 +TGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCDCCCCCBCCACCCCBCC +@61DFRAAXX100204:1:102:17677:10400/2 +CAATCCCTACAAAGTCAACTAAACAGAATGTAGCCAGTGAAAAGCAAAGACGACTTCTGTATAACTTAGAAATGGA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCBCCCCACDCC;@BBB@C +@61DFRAAXX100204:1:102:17711:7491/2 +TATAAACCAAGAGCATGAAGGGGATCTTGAGCCCCAAACACATGATGTGGATAAAAGTCTCCAAGATGATACAGAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCDCCCCCCCADC=DCCBCDA +@61DFRAAXX100204:1:102:17798:2084/2 +AGTGAAGTTAAACACCCAGAGACTATAAACAGATATGGAAGTTTAAACTCCTTAGAATCCACATCATCATCAGGAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCDC +@61DFRAAXX100204:1:102:18807:10059/2 +CTACAATATCTATTTAGCCAGCAAAAATCTCATCAATCAGACAACAGCCAAAGCTACTCTTACTCAAATGCTGAAC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCACC +@61DFRAAXX100204:1:102:19518:11565/2 +CTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCBCC@BCCCDBCCDABDDDDCDBCBDCBDDA +@61DFRAAXX100204:1:102:2639:2051/2 +CAGGAGTCTATTGGAGAAACCAGCTCTCAAAGTGTGGTAGTTGCTGTGGATAGAATATTCACCGGATCCACAAGGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCDCCACCDCCCCCACCBCB@<A88>>5?>@>@17>A1;5;:=; +@61DFRAAXX100204:1:102:3101:2926/2 +GAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACC ++ +CCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCACCCCCCCCCCCDBCC +@61DFRAAXX100204:1:102:5977:14503/2 +GAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCDCDCDCCCCCCDCDCCCCCDBCDCB +@61DFRAAXX100204:1:102:6251:21399/2 +GTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCDCCCCDCCCCDCACCBCBCCBDDCC@D<BCBDDBDAB +@61DFRAAXX100204:1:102:7093:4246/2 +GAAGATTTTTGCACACTCAGGCTATCTGAGACACCGGAAATCATCATCTTTCTGTGAAAATGTACAGAGATGCAGG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCBCCBCB@ABBBADB@C= +@61DFRAAXX100204:1:102:7907:21314/2 +GACTCTCTGAGGCAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGACTTCT ++ +@@@9@####################################################################### +@61DFRAAXX100204:1:102:8037:6949/2 +CTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAA ++ +CCCCCCCCCCCDCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCDCCCCCCCCADCBCCABCAD@C@ +@61DFRAAXX100204:1:102:8724:1888/2 +TGAACTCCTTAGAATCCACATCATCATCAGGAATTGGCAGCTACAGTACACAGATGTCTGGCACTGATAATCCAGA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@=B?@99;>?BB==<@=@A?B=<<BBB>DB2(?=;@ +@61DFRAAXX100204:1:102:8903:16361/2 +GCATTTTCAGCATTCAGCTGGAAAGAGATGCATATGTCCAAGCACTAGCCAGATTTACCTTACTTACAGTGAGTTC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCBCBCC +@61DFRAAXX100204:1:102:9691:18717/2 +CTAGAAGGGATAAGATGTGCTATCAGGATTGCATGCATTTTCAGCATTCAGCTGGAAAGAGATGCATATGTCCAAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:10201:1449/2 +GAGACTATGAAGAAAAGCCACTTGATATTGTCCAGAGCATTGTAGAAGAAATGTTGAACATCATTGTTGGAGACAT ++ +CCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCBCCCCCCCDCBCCCCDCCCCCCCDCCCCDCA@BCBBB? +@61DFRAAXX100204:1:103:11572:6697/2 +AGCTCATTTGACCATAAGTGGATGGTTATTCAGACACTGACAAGGATCTGTGCAGATGCTCAGAGTGTGGTGGACA ++ +CCCCCCCCCCCCCCCCCCAC???AAACCCCCCCCCCCCCCCCCCCBCCCCCCCC@CABCCCCAACBC>CB<A?:BB +@61DFRAAXX100204:1:103:12517:20251/2 +CAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACGACCTTTTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCCCCDDCDCCCCCCCDCDDDBCD +@61DFRAAXX100204:1:103:13105:12342/2 +TCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGC ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCBCDD@BAAA +@61DFRAAXX100204:1:103:13548:1359/2 +GGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCBDCDCCCBDCCCBDDBCCDDCDCADDBDC@B +@61DFRAAXX100204:1:103:13762:1440/2 +GAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCBCCCCCCCCDCCCDDCBCCCCB@BCC> +@61DFRAAXX100204:1:103:13776:4298/2 +CCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCBCCCCCCCC +@61DFRAAXX100204:1:103:13798:6365/2 +GTTTATTAATGCTATCAAGCAGTATCTATGTGTTGCACTCTCAAAAAACGGAGTCTCATCTGTTCCAGAGGTTTTT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCCCCCCDCCDDCDCCBDDC@ +@61DFRAAXX100204:1:103:14748:1375/2 +TAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTAAATACCCATA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@BCCB=CCBBBC@@CCCACCCACCCCBCCCDD>DC +@61DFRAAXX100204:1:103:16156:9928/2 +CTCATGTTGAGCAGAAAGGCTGTTCCCACAGCATCAGCCTACCTTTAGGGTCCTTCCCTGTCCTCTAAGCAGGGTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCDCCCDCCDCCA@ACBABB?B +@61DFRAAXX100204:1:103:16292:7311/2 +CACCATTGATTCTTTCCAGGATGCAGTGAAGTGTTTGTCTGAATTCACATGTAATGCAGCTTTCCCAGACACAAGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCC5CCCCDCCCCCBCCBCCCBDDDBDBBBBCD +@61DFRAAXX100204:1:103:1757:15756/2 +TGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +@61DFRAAXX100204:1:103:19512:1223/2 +TGTCACTCTTGTATTTGAAAAACACTTTCCGGCCACCATTGATTCTTTCCAGGATGCAGTGAAGTGTTTGTCTGAA ++ +CCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCC@CBA8=A=CCACCCBCCA# +@61DFRAAXX100204:1:103:2005:9846/2 +TTTAATTCCAACAATGAACAGAGGGCTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA ++ +CCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBDDBCDCCDBDCBCCDDDCDADBBDDC +@61DFRAAXX100204:1:103:2755:14644/2 +GCTGCATCAGACCAAGATGAAAGCATAGTAGAACTTGCATTTCAGACAACAGGGCACATTGTCACTCTTGTATTTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCACCCCC>CCC@CBACDCCDCC +@61DFRAAXX100204:1:103:3597:13520/2 +CACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCACACDDCCDDCCB@A?B@BB@ABBBBADABD<?>AA +@61DFRAAXX100204:1:103:4062:11566/2 +CAACAATTCGAGATATGGTTGTACGGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATG ++ +CCCCCCCBCCCCCCCCCCCCC?CCCC=CCCCCA=@A@CCACBCC?ABAABCCCCACC>BC<CCCACCCCB@C@B@? +@61DFRAAXX100204:1:103:5147:16732/2 +GGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCBCCCBCCCCCCCBCCBBCCBC +@61DFRAAXX100204:1:103:6646:12936/2 +CTCCAATGATACTCAGGAATCTGGAAATTCTTCAGGACCTTCACCTGGTGCTAAGTTTTCCCACATTTTACAAAAG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCC@CDCCDCCCCCDCCCDBDBADDC +@61DFRAAXX100204:1:103:7220:15954/2 +GATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBCCCCCCCCCCCCCBCDC +@61DFRAAXX100204:1:103:7253:3680/2 +GTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTT ++ +CCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@BCCCCCCCBCDCCCBCCCCCCB=CDA +@61DFRAAXX100204:1:103:8055:11636/2 +AAATGACCTGTCGAAAATTGCACAAGGAAGGGGCAGCCAAGAACTTGGTATGAGTAATGTTCAGGAATTGAGCCTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCDCCCCDACCCCCCCCCACCCCC +@61DFRAAXX100204:1:103:8348:14452/2 +AACATTTGGGTTGAACTTTTAGTCTTTGGGGGAGTGGTGGTCATTTTGAGGGCTTGCTGTGCCCTGAATCTGTTGT ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@CCCCCDCCCCCCCCCCCCCACBCCDCCCCCAB@CBCCDCBB +@61DFRAAXX100204:1:104:12460:3347/2 +CACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTTACATTG ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCBCCC@@@BBCCCACBCCC@ACBC +@61DFRAAXX100204:1:104:12993:12947/2 +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTTGCCATTGTGCAAAA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCC@CCACBCDDCBCC,BBC?BBBBB@BBBD +@61DFRAAXX100204:1:104:13501:6860/2 +CTGAGCTACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTA ++ +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samples.tsv Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,4 @@ +ConditionA CondA_replicate1 +ConditionA CondA_replicate2 +ConditionB CondB_replicate1 +ConditionB CondB_replicate2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/supertranscripts/trinity_genes.fasta Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,14 @@ +>TRINITY_DN2_c3_g1 +GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACCAA +>TRINITY_DN0_c0_g1 +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC +>TRINITY_DN2_c0_g1 +TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA +>TRINITY_DN3_c0_g1 +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT +>TRINITY_DN2_c2_g1 +ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGAGTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGCTACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC +>TRINITY_DN2_c1_g1 +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTG +>TRINITY_DN1_c0_g1 +CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATGTATATGGTACAGATGTAAAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/supertranscripts/trinity_genes.gtf Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,14 @@ +TRINITY_DN2_c3_g1 Trinity_gene exon 1 202 . + . gene_id "TRINITY_DN2_c3_g1"; transcript_id "TRINITY_DN2_c3_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_DN3_c0_g1 Trinity_gene exon 1 216 . + . gene_id "TRINITY_DN3_c0_g1"; transcript_id "TRINITY_DN3_c0_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_c1_g1 Trinity_gene exon 1 541 . + . gene_id "TRINITY_DN2_c1_g1"; transcript_id "TRINITY_DN2_c1_g1_i1" + +TRINITY_DN1_c0_g1 Trinity_gene exon 1 380 . + . gene_id "TRINITY_DN1_c0_g1"; transcript_id "TRINITY_DN1_c0_g1_i1" +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trinityStats.xml Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,52 @@ +<tool id="trinity_stats" name="Trinity Stats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="bio_tools"/> + <expand macro="requirements" /> + <command detect_errors="aggressive"><![CDATA[ + #if $input.ext.endswith(".gz") + gunzip -c '$input' > input && + #else + ln -s '$input' input && + #end if + TrinityStats.pl input > '$statsfile' + ]]> + </command> + + <inputs> + <param name='input' type="data" format="fasta,fasta.gz" label='Trinity Assembly' help='Trinity Assembled fasta file'/> + </inputs> + + <outputs> + <data name='statsfile' format='txt'/> + </outputs> + + <tests> + <test> + <param name="input" value="count/contig_exn50_statistic/Trinity.fasta"/> + <output name="statsfile" file="count/trinityStats/statsfile.txt"/> + </test> + <test> + <param name="input" value="count/contig_exn50_statistic/Trinity.fasta.gz"/> + <output name="statsfile" file="count/trinityStats/statsfile.txt"/> + </test> + </tests> + <help> +<![CDATA[ +Trinity_ assembles transcript sequences from Illumina RNA-Seq data. +This tool computes basic statistics of the assembly (such as stats for genes, transcripts, reconstruction size and N metrics). + +**Inputs** + +It takes as input a transcriptome assembled with Trinity. + +.. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki +]]> + </help> + <expand macro="citation" /> + <creator> + <person givenName="Paul" familyName="Zierep" email="zierep@informatik.uni-freiburg.de" /> + </creator> +</tool>