| Previous changeset 4:1fc32fd3fb3f (2017-03-23) Next changeset 6:74217fbfba4d (2017-08-28) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933 |
|
modified:
README.rst abundance_estimates_to_matrix.xml macros.xml test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results test-data/count/trinotate/genes.lengths.txt test-data/filtered/Trinity_filtered_exp.fasta |
|
added:
test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.count_matrix test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.count_matrix test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.count_matrix test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.count_matrix test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.count_matrix test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.count_matrix test-data/filtered/Trinity_filtered_hi_iso.fasta |
|
removed:
tool_dependencies.xml |
| b |
| diff -r 1fc32fd3fb3f -r 8b5039bdf1f6 README.rst --- a/README.rst Thu Mar 23 10:18:33 2017 -0400 +++ b/README.rst Fri Mar 31 11:37:24 2017 -0400 |
| b |
| @@ -6,13 +6,25 @@ trinity requires a large amount of memory to perform the assembly: "roughly ~1G of RAM per 1M reads to be assembled" -By default, this tool is configured to limit the memory consumption to 30G. +By default, this tool is configured to limit the memory consumption to 1G. You might need to lower this limit if the machine(s) executing the jobs have less memory available. If you have a lot of reads to assemble and a machine with enough memory, you can increase it. -In both cases, you can edit the TRINITY_MEM_OPTIONS in the file: - -<tool_dependency_dir>/environment_settings/TRINITY_MEM_OPTIONS/iuc/trinity/<hash_string>/env.sh +In both cases, you can set the TRINITY_MAX_MEMORY environmental variable in the destination section of the job_conf.xml file: -to lower the maximum memory usage to 2G for example: +<?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="TRINITY_MAX_MEMORY">1G</env> + </destination> + </destinations> +</job_conf> -TRINITY_MEM_OPTIONS='--max_memory 2G --bflyHeapSpaceMax 2G' + |
| b |
| diff -r 1fc32fd3fb3f -r 8b5039bdf1f6 abundance_estimates_to_matrix.xml --- a/abundance_estimates_to_matrix.xml Thu Mar 23 10:18:33 2017 -0400 +++ b/abundance_estimates_to_matrix.xml Fri Mar 31 11:37:24 2017 -0400 |
| [ |
| @@ -1,17 +1,17 @@ -<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.1"> +<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.0"> <description>for a de novo assembly of RNA-Seq data by Trinity</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> - <requirement type="package" version="3.14.0">bioconductor-edger</requirement> - <requirement type="package" version="0.7.2">salmon</requirement> + <requirement type="package" version="3.16.5">bioconductor-edger</requirement> + <!-- Cannot update to salmon 0.8.2 because in Bioconda it requires icu 58, while r-base 3.3.1 requires icu 54 --> + <requirement type="package" version="0.8.1">salmon</requirement> </expand> - <expand macro="stdio"/> - <command><![CDATA[ + <command detect_errors="aggressive"><![CDATA[ #import re #for $entry in $samples: - ln -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' && + ln -f -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' && #end for abundance_estimates_to_matrix.pl |
| b |
| diff -r 1fc32fd3fb3f -r 8b5039bdf1f6 macros.xml --- a/macros.xml Thu Mar 23 10:18:33 2017 -0400 +++ b/macros.xml Fri Mar 31 11:37:24 2017 -0400 |
| b |
| @@ -2,18 +2,12 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.2.0">trinity</requirement> + <requirement type="package" version="2.4.0">trinity</requirement> <yield/> </requirements> </xml> - <token name="@WRAPPER_VERSION@">2.2.0</token> - - <xml name="stdio"> - <stdio> - <exit_code range="1:" level="fatal" description="Error in Trinity execution" /> - </stdio> - </xml> + <token name="@WRAPPER_VERSION@">2.4.0</token> <xml name="citation"> <citations> |
| b |
| diff -r 1fc32fd3fb3f -r 8b5039bdf1f6 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results --- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results Thu Mar 23 10:18:33 2017 -0400 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results Fri Mar 31 11:37:24 2017 -0400 |
| b |
| b'@@ -1,39 +1,38 @@\n-id\tbaseMeanA\tbaseMeanB\tbaseMean\tlog2FoldChange\tlfcSE\tstat\tpvalue\tpadj\n-TR4277|c0_g1_i1\t3852.97388871986\t161.116814813422\t2007.04535176664\t-4.57259674791206\t0.121601866332754\t-37.6030145409076\t0\t0\n-TR131|c0_g1_i1\t26.1866396538608\t1340.30918254958\t683.247911101723\t5.67372481552909\t0.187406695960058\t30.274931140872\t2.45144211418965e-201\t4.04487948841292e-200\n-TR4761|c0_g1_i1\t1645.20640957447\t193.196157329029\t919.201283451752\t-3.08847487551254\t0.143642016580712\t-21.5011940728159\t1.51733402752078e-102\t1.66906743027286e-101\n-TR3091|c0_g1_i1\t16.7444693227929\t328.569936894811\t172.657203108802\t4.29039998257063\t0.240421038467916\t17.8453599980735\t3.14072644239509e-71\t2.59109931497595e-70\n-TR3638|c0_g1_i1\t583.00358519031\t183.754416330029\t383.37900076017\t-1.66018915730897\t0.144484444213305\t-11.4904352945982\t1.47367477630653e-30\t9.72625352362312e-30\n-TR2487|c0_g1_i1\t342.210853400436\t920.407318992504\t631.30908619647\t1.42690938766606\t0.124693202553469\t11.4433614539188\t2.5385551583546e-30\t1.39620533709503e-29\n-TR3788|c0_g1_i1\t19.5075441237117\t134.95369713876\t77.2306206312357\t2.77038513264018\t0.262760026053246\t10.5434040871909\t5.44900939296595e-26\t2.56881871382681e-25\n-TR1479|c0_g1_i1\t129.593534475689\t371.064629188207\t250.329081831948\t1.51441163103673\t0.145431922863633\t10.4131995315551\t2.1584296431011e-25\t8.90352227779205e-25\n-TR2107|c1_g1_i1\t48.9228907410258\t7.40521775805688\t28.1640542495414\t-2.6949883047084\t0.431525668867458\t-6.24525607429428\t4.23106352657394e-10\t1.55138995974378e-09\n-TR3854|c0_g1_i1\t1573.69549271337\t2374.56159860719\t1974.12854566028\t0.593513416954248\t0.111306645736399\t5.33223701987958\t9.70102011419466e-08\t3.20133663768424e-07\n-TR2122|c0_g2_i2\t119.534640490118\t199.143666337033\t159.339153413576\t0.738656537188098\t0.168436715892782\t4.38536534788702\t1.15791268060543e-05\t3.47373804181628e-05\n-TR1449|c0_g1_i1\t180.814952011467\t104.755290736358\t142.785121373912\t-0.784194659361461\t0.185749133486416\t-4.2217944420118\t2.42365089281258e-05\t6.61949164163031e-05\n-TR4163|c0_g1_i1\t347.283468916919\t232.772947466212\t290.028208191566\t-0.576744528291395\t0.137147958253208\t-4.20527243450891\t2.60767852549073e-05\t6.61949164163031e-05\n-TR2672|c0_g1_i1\t18.3155337236093\t2.26581902751323\t10.2906763755613\t-2.88818323474529\t0.724350842979802\t-3.98727117216294\t6.68376171815065e-05\t0.000157545811927837\n-TR127|c1_g1_i1\t13.461799216177\t1.21881296083961\t7.34030608850831\t-3.33218181130749\t0.914685635912973\t-3.64298036448506\t0.000269499403689035\t0.000576210779000196\n-TR5055|c0_g2_i1\t23.3590211688541\t5.52768338415684\t14.4433522765055\t-2.04478780320925\t0.562727305023446\t-3.63370994255211\t0.00027937492315161\t0.000576210779000196\n-TR2844|c0_g1_i1\t158.206282615139\t231.762548186068\t194.984415400603\t0.550641897280872\t0.154759496937021\t3.55804915484414\t0.000373619406412113\t0.000725261200682336\n-TR5212|c0_g1_i1\t65.7079302129484\t107.875371765755\t86.7916509893515\t0.713884138135847\t0.209708011296715\t3.40418152707468\t0.000663626354411326\t0.00121664831642076\n-TR1894|c2_g1_i1\t13.3497721959996\t2.96749216411516\t8.15863218005739\t-2.04982326482473\t0.714661961266818\t-2.8682417365424\t0.00412760030232129\t0.00716898999876856\n-TR24|c0_g1_i1\t69.9065207344592\t41.2394742844514\t55.5729975094553\t-0.760369639593845\t0.269117661787534\t-2.8254170853868\t0.00472191070589177\t0.00779115266472142\n-TR4669|c0_g2_i1\t0\t167.096667347181\t83.5483336735905\t4.37844609928899\t2.00484514683835\t2.18393231327309\t0.0289672221614669\t0.0455199205394479\n-TR2779|c0_g1_i1\t155.915506826481\t205.619872596257\t180.767689711369\t0.402360429872658\t0.188906223389576\t2.12994798505331\t0.0331759079102528\t0.0497638618653791\n-TR1492|c0_g1_i2\t1640.89375005483\t1435.64893261411\t1538.27134133447\t-0.192484740220531\t0.101376439014472\t-1.89871277874588\t0.0576022504671541\t0.0796285639028554\n-TR3807|c0_g1_i1\t3.48709246029019\t0.350050334268211\t1.9185713972792\t-2.70461238638113\t1.4262081182078\t-1.89636586123194\t0.0579116828384403\t0.0796285639028554\n-TR4084|c0_g1_i1\t93.2264707954139\t121.352438036668\t107.289454416041\t0.3802042'..b'.88216980025882e-05\t0.000181885916149697\n+TR127|c1_g1_i1\twt_37\twt_GSNO\t13.461799216177\t1.21881296083961\t7.34030608850831\t3.33150202228086\t0.915899815581865\t3.63740877070095\t0.000275394687501815\t0.000667511143840185\n+TR5055|c0_g2_i1\twt_37\twt_GSNO\t23.3590211688541\t5.52768338415684\t14.4433522765055\t2.04460941512382\t0.563987307210913\t3.62527558507482\t0.000288653467606567\t0.000667511143840185\n+TR2844|c0_g1_i1\twt_37\twt_GSNO\t158.206282615139\t231.762548186068\t194.984415400603\t-0.550639207704626\t0.154913717539885\t-3.55448966333699\t0.000378713397971402\t0.000824258572055403\n+TR5212|c0_g1_i1\twt_37\twt_GSNO\t65.7079302129484\t107.875371765755\t86.7916509893515\t-0.713874873222434\t0.210087143945163\t-3.39799408862815\t0.000678818868686303\t0.00139534989674407\n+TR1894|c2_g1_i1\twt_37\twt_GSNO\t13.3497721959996\t2.96749216411516\t8.15863218005739\t2.04972102673103\t0.716146945354672\t2.86215146210796\t0.00420775772107294\t0.00819405450945783\n+TR24|c0_g1_i1\twt_37\twt_GSNO\t69.9065207344592\t41.2394742844514\t55.5729975094553\t0.760351613917761\t0.269735390145923\t2.81887969356346\t0.00481915767774413\t0.00891544170382664\n+TR2779|c0_g1_i1\twt_37\twt_GSNO\t155.915506826481\t205.619872596257\t180.767689711369\t-0.402350189521528\t0.18910416680051\t-2.12766432558821\t0.0333649247395808\t0.0587858197792614\n+TR3807|c0_g1_i1\twt_37\twt_GSNO\t3.48709246029019\t0.350050334268211\t1.9185713972792\t2.6523001983829\t1.38324824664578\t1.91744338358239\t0.055181627150862\t0.092164962039527\n+TR1492|c0_g1_i2\twt_37\twt_GSNO\t1640.89375005483\t1435.64893261411\t1538.27134133447\t0.192484568368337\t0.101250195527162\t1.90107848548993\t0.057291733159706\t0.092164962039527\n+TR4084|c0_g1_i1\twt_37\twt_GSNO\t93.2264707954139\t121.352438036668\t107.289454416041\t-0.380198430346905\t0.213412163689062\t-1.78152183912463\t0.0748272403991533\t0.115358662282028\n+TR1891|c0_g1_i1\twt_37\twt_GSNO\t107.628573623499\t135.399287466928\t121.513930545214\t-0.328810062058933\t0.189329296532127\t-1.73670989161013\t0.0824383909023624\t0.122008818535496\n+TR4669|c0_g2_i1\twt_37\twt_GSNO\t0\t167.096667347181\t83.5483336735905\t-3.46077834317638\t2.04233842282563\t-1.69451757088734\t0.0901669757000038\t0.128314542342313\n+TR1837|c2_g1_i1\twt_37\twt_GSNO\t0.308903905435236\t2.22601224010275\t1.26745807276899\t-2.41951712666755\t1.51166579847997\t-1.60056351681732\t0.1094736282342\t0.150019416469089\n+TR5075|c0_g1_i1\twt_37\twt_GSNO\t15.8633018853512\t9.23822794034992\t12.5507649128506\t0.764028730403883\t0.508108615055784\t1.50367206491864\t0.132665825459353\t0.172493073735055\n+TR4859|c0_g1_i1\twt_37\twt_GSNO\t7.32690480813971\t3.17910584569163\t5.25300532691567\t1.18248087647214\t0.791530422232021\t1.49391715499409\t0.135197274008557\t0.172493073735055\n+TR939|c0_g1_i1\twt_37\twt_GSNO\t84.2568220960088\t96.9171174594069\t90.5869697777078\t-0.202690605185084\t0.202556787736977\t-1.00066064163834\t0.316990901598642\t0.384256032989688\n+TR2278|c0_g1_i1\twt_37\twt_GSNO\t486.5272515724\t448.140178813055\t467.333715192727\t0.118822806572317\t0.119966033346418\t0.99047041281427\t0.321944243856225\t0.384256032989688\n+TR2011|c5_g1_i1\twt_37\twt_GSNO\t5.60408627995835\t7.88255079488408\t6.74331853742122\t-0.48861876789566\t0.691406970296359\t-0.706702114510391\t0.479751615248569\t0.554712805131158\n+TR2182|c3_g2_i6\twt_37\twt_GSNO\t2.24974854180929\t1.3031439398571\t1.77644624083319\t0.779605221657958\t1.28583289420755\t0.606303684693354\t0.544313112275579\t0.605163179078445\n+TR3249|c0_g1_i1\twt_37\twt_GSNO\t1.12573841927462\t2.128954842887\t1.62734663108081\t-0.761341397480685\t1.29336792501876\t-0.58865028485196\t0.556095894288301\t0.605163179078445\n+TR1678|c0_g1_i1\twt_37\twt_GSNO\t0.595141051681226\t0.700100668536423\t0.647620860108824\t-0.247288262290953\t1.73789746083653\t-0.14229162989393\t0.886849657633351\t0.935371730620685\n+TR1122|c0_g1_i1\twt_37\twt_GSNO\t1.41370386226057\t1.3031439398571\t1.35842390105883\t0.162148276801819\t1.43591594510694\t0.112923237153511\t0.910091413576882\t0.935371730620685\n+TR1982|c2_g1_i1\twt_37\twt_GSNO\t5.73684100209948\t5.71221669652109\t5.72452884931028\t-0.0101267142582557\t0.715373046105777\t-0.0141558510114153\t0.988705642243408\t0.988705642243408\n' |
| b |
| diff -r 1fc32fd3fb3f -r 8b5039bdf1f6 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix Fri Mar 31 11:37:24 2017 -0400 |
| b |
| @@ -0,0 +1,38 @@ +wt_37_1 wt_37_2 wt_37_3 wt_GSNO_1 wt_GSNO_2 wt_GSNO_3 +TR24|c0_g1_i1 85 90 67 35 34 36 +TR2779|c0_g1_i1 217 186 137 186 197 147 +TR127|c1_g1_i1 16 9 23 0 1 2 +TR2107|c1_g1_i1 47 59 65 6 7 6 +TR2011|c5_g1_i1 4 11 4 5 7 8 +TR4163|c0_g1_i1 425 368 422 216 210 172 +TR5055|c0_g2_i1 27 36 17 7 3 4 +TR1449|c0_g1_i1 207 196 230 113 91 66 +TR1982|c2_g1_i1 6 7 7 3 8 4 +TR1492|c0_g1_i2 1921 1895 1906 1263 1319 1104 +TR1122|c0_g1_i1 0 2 3 0 0 3 +TR2278|c0_g1_i1 598 497 610 406 413 333 +TR4084|c0_g1_i1 86 95 148 111 127 77 +TR4761|c0_g1_i1 1875 2089 1746 174 165 155 +TR3638|c0_g1_i1 712 647 676 184 174 117 +TR3854|c0_g1_i1 1864 1878 1734 2173 2151 1775 +TR131|c0_g1_i1 31 32 28 1233 1208 1001 +TR5075|c0_g1_i1 21 13 22 8 10 6 +TR2182|c3_g2_i6 4 1 3 0 0 3 +TR3788|c0_g1_i1 22 17 30 132 125 91 +TR4859|c0_g1_i1 8 6 12 1 3 4 +TR2487|c0_g1_i1 424 386 383 866 806 689 +TR2122|c0_g2_i2 136 145 135 157 201 155 +TR4277|c0_g1_i1 4284 4466 4701 134 164 118 +TR4669|c0_g2_i1 0 0 0 0 218 209 +TR3091|c0_g1_i1 19 22 17 308 284 250 +TR3807|c0_g1_i1 2 6 4 0 1 0 +TR1894|c2_g1_i1 11 21 14 2 5 1 +TR5212|c0_g1_i1 78 64 89 98 108 73 +TR939|c0_g1_i1 99 96 99 89 88 72 +TR1891|c0_g1_i1 124 115 138 139 111 97 +TR2672|c0_g1_i1 22 14 29 4 2 0 +TR2844|c0_g1_i1 178 166 211 214 223 161 +TR1837|c2_g1_i1 0 1 0 1 4 1 +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 |
| b |
| diff -r 1fc32fd3fb3f -r 8b5039bdf1f6 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.count_matrix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.count_matrix Fri Mar 31 11:37:24 2017 -0400 |
| b |
| @@ -0,0 +1,38 @@ +wt_37_1 wt_37_2 wt_37_3 wt_GSNO_1 wt_GSNO_2 wt_GSNO_3 +TR24|c0_g1_i1 85 90 67 35 34 36 +TR2779|c0_g1_i1 217 186 137 186 197 147 +TR127|c1_g1_i1 16 9 23 0 1 2 +TR2107|c1_g1_i1 47 59 65 6 7 6 +TR2011|c5_g1_i1 4 11 4 5 7 8 +TR4163|c0_g1_i1 425 368 422 216 210 172 +TR5055|c0_g2_i1 27 36 17 7 3 4 +TR1449|c0_g1_i1 207 196 230 113 91 66 +TR1982|c2_g1_i1 6 7 7 3 8 4 +TR1492|c0_g1_i2 1921 1895 1906 1263 1319 1104 +TR1122|c0_g1_i1 0 2 3 0 0 3 +TR2278|c0_g1_i1 598 497 610 406 413 333 +TR4084|c0_g1_i1 86 95 148 111 127 77 +TR4761|c0_g1_i1 1875 2089 1746 174 165 155 +TR3638|c0_g1_i1 712 647 676 184 174 117 +TR3854|c0_g1_i1 1864 1878 1734 2173 2151 1775 +TR131|c0_g1_i1 31 32 28 1233 1208 1001 +TR5075|c0_g1_i1 21 13 22 8 10 6 +TR2182|c3_g2_i6 4 1 3 0 0 3 +TR3788|c0_g1_i1 22 17 30 132 125 91 +TR4859|c0_g1_i1 8 6 12 1 3 4 +TR2487|c0_g1_i1 424 386 383 866 806 689 +TR2122|c0_g2_i2 136 145 135 157 201 155 +TR4277|c0_g1_i1 4284 4466 4701 134 164 118 +TR4669|c0_g2_i1 0 0 0 0 218 209 +TR3091|c0_g1_i1 19 22 17 308 284 250 +TR3807|c0_g1_i1 2 6 4 0 1 0 +TR1894|c2_g1_i1 11 21 14 2 5 1 +TR5212|c0_g1_i1 78 64 89 98 108 73 +TR939|c0_g1_i1 99 96 99 89 88 72 +TR1891|c0_g1_i1 124 115 138 139 111 97 +TR2672|c0_g1_i1 22 14 29 4 2 0 +TR2844|c0_g1_i1 178 166 211 214 223 161 +TR1837|c2_g1_i1 0 1 0 1 4 1 +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 |
| b |
| diff -r 1fc32fd3fb3f -r 8b5039bdf1f6 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.count_matrix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.count_matrix Fri Mar 31 11:37:24 2017 -0400 |
| b |
| @@ -0,0 +1,38 @@ +wt_37_1 wt_37_2 wt_37_3 wt_GSNO_1 wt_GSNO_2 wt_GSNO_3 +TR24|c0_g1_i1 85 90 67 35 34 36 +TR2779|c0_g1_i1 217 186 137 186 197 147 +TR127|c1_g1_i1 16 9 23 0 1 2 +TR2107|c1_g1_i1 47 59 65 6 7 6 +TR2011|c5_g1_i1 4 11 4 5 7 8 +TR4163|c0_g1_i1 425 368 422 216 210 172 +TR5055|c0_g2_i1 27 36 17 7 3 4 +TR1449|c0_g1_i1 207 196 230 113 91 66 +TR1982|c2_g1_i1 6 7 7 3 8 4 +TR1492|c0_g1_i2 1921 1895 1906 1263 1319 1104 +TR1122|c0_g1_i1 0 2 3 0 0 3 +TR2278|c0_g1_i1 598 497 610 406 413 333 +TR4084|c0_g1_i1 86 95 148 111 127 77 +TR4761|c0_g1_i1 1875 2089 1746 174 165 155 +TR3638|c0_g1_i1 712 647 676 184 174 117 +TR3854|c0_g1_i1 1864 1878 1734 2173 2151 1775 +TR131|c0_g1_i1 31 32 28 1233 1208 1001 +TR5075|c0_g1_i1 21 13 22 8 10 6 +TR2182|c3_g2_i6 4 1 3 0 0 3 +TR3788|c0_g1_i1 22 17 30 132 125 91 +TR4859|c0_g1_i1 8 6 12 1 3 4 +TR2487|c0_g1_i1 424 386 383 866 806 689 +TR2122|c0_g2_i2 136 145 135 157 201 155 +TR4277|c0_g1_i1 4284 4466 4701 134 164 118 +TR4669|c0_g2_i1 0 0 0 0 218 209 +TR3091|c0_g1_i1 19 22 17 308 284 250 +TR3807|c0_g1_i1 2 6 4 0 1 0 +TR1894|c2_g1_i1 11 21 14 2 5 1 +TR5212|c0_g1_i1 78 64 89 98 108 73 +TR939|c0_g1_i1 99 96 99 89 88 72 +TR1891|c0_g1_i1 124 115 138 139 111 97 +TR2672|c0_g1_i1 22 14 29 4 2 0 +TR2844|c0_g1_i1 178 166 211 214 223 161 +TR1837|c2_g1_i1 0 1 0 1 4 1 +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 |
| b |
| diff -r 1fc32fd3fb3f -r 8b5039bdf1f6 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results --- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results Thu Mar 23 10:18:33 2017 -0400 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results Fri Mar 31 11:37:24 2017 -0400 |
| b |
| b'@@ -1,39 +1,39 @@\n-id\tbaseMeanA\tbaseMeanB\tbaseMean\tlog2FoldChange\tlfcSE\tstat\tpvalue\tpadj\n-TR4277|c0_g1_i1\t4705.34614971641\t162.902721493704\t2434.12443560506\t-4.84860951090545\t0.124597307945428\t-38.9142397284305\t0\t0\n-TR131|c0_g1_i1\t32.0461070493257\t1436.30905989883\t734.177583474076\t5.48367743370229\t0.196017912869615\t27.9753893581648\t3.23827538807456e-172\t6.15272323734167e-171\n-TR4761|c0_g1_i1\t2012.6141923276\t384.620292965437\t1198.61724264652\t-2.38450946693381\t0.143863830576436\t-16.5747669680385\t1.06073316501088e-61\t1.34359534234711e-60\n-TR3091|c0_g1_i1\t20.4914097091341\t321.651020117047\t171.071214913091\t3.96886910507283\t0.256323110469072\t15.4838519937191\t4.45952081812589e-54\t4.2365447772196e-53\n-TR2779|c0_g1_i1\t191.51955185349\t1058.15934185376\t624.839446853626\t2.46616535412611\t0.177102083131526\t13.9251064161374\t4.4587691300744e-44\t3.38866453885655e-43\n-TR1492|c0_g1_i2\t2006.11782336441\t890.823502721036\t1448.47066304272\t-1.17029110983798\t0.12207086547883\t-9.58698134274255\t9.06997941755552e-22\t5.74432029778516e-21\n-TR5075|c0_g1_i1\t19.3833722195684\t136.98672801182\t78.1850501156942\t2.80049241151413\t0.293976352213923\t9.52625063350759\t1.63066468983638e-21\t8.85217974482605e-21\n-TR1891|c0_g1_i1\t131.416087212132\t376.595292171713\t254.005689691923\t1.51493508389526\t0.17090866237033\t8.86400409952692\t7.71909159725621e-19\t3.6665685086967e-18\n-TR2487|c0_g1_i1\t418.818667162757\t965.862817209246\t692.340742186001\t1.20547893236143\t0.136832960243688\t8.80985787499278\t1.25304626500959e-18\t5.29063978559604e-18\n-TR3638|c0_g1_i1\t713.131183384274\t326.063958913919\t519.597571149096\t-1.1281436752687\t0.141731779309567\t-7.95970868893582\t1.72444792020844e-15\t6.55290209679206e-15\n-TR2107|c1_g1_i1\t59.5986596731862\t1.89840873462066\t30.7485342039034\t-4.81058600791914\t0.641850436461167\t-7.49487066557473\t6.63637683134955e-14\t2.29256654173894e-13\n-TR2122|c0_g2_i2\t146.135958637131\t360.821667264163\t253.478812950647\t1.30334955915215\t0.177300500792357\t7.35107658087526\t1.96616724778278e-13\t6.22619628464548e-13\n-TR1479|c0_g1_i1\t158.005105094407\t334.827472148091\t246.416288621249\t1.07882286721986\t0.173458235018578\t6.2194963940704\t4.98753084614221e-10\t1.45789363194926e-09\n-TR24|c0_g1_i1\t85.6614643869141\t199.923709280262\t142.792586833588\t1.22623657127381\t0.213504266341901\t5.74338205172044\t9.2804014146814e-09\t2.51896609827067e-08\n-TR4163|c0_g1_i1\t424.593720981574\t227.471218917767\t326.03246994967\t-0.900786056392834\t0.160721595544993\t-5.60463609969988\t2.08692952426197e-08\t5.28688812813031e-08\n-TR2278|c0_g1_i1\t594.657329919233\t348.341653317169\t471.499491618201\t-0.772446091346236\t0.159105007190944\t-4.85494520244241\t1.20420038267752e-06\t2.79113819122931e-06\n-TR1449|c0_g1_i1\t220.782434528097\t117.26089394399\t169.021664236043\t-0.913694497348233\t0.188477876305836\t-4.84775462911953\t1.24866708554995e-06\t2.79113819122931e-06\n-TR127|c1_g1_i1\t16.3791628279609\t1.58772512712498\t8.98344397754296\t-3.19771077466237\t0.834376974262452\t-3.83245328346816\t0.00012687169720824\t0.000267840249661839\n-TR1894|c2_g1_i1\t16.2826445742552\t1.67571344127509\t8.97917900776516\t-3.15659686337855\t0.834779400611257\t-3.7813545244015\t0.00015597736029041\t0.000307529893573321\n-TR5055|c0_g2_i1\t28.6665933385886\t6.05959103586122\t17.3630921872249\t-2.17768048931004\t0.577307428800381\t-3.77213314894485\t0.000161857838722801\t0.000307529893573321\n-TR4084|c0_g1_i1\t113.2594381118\t173.837287636503\t143.548362874151\t0.609755827935052\t0.219803235717165\t2.7740985065373\t0.00553549140639085\t0.00984268771318224\n-TR2090|c0_g1_i1\t0\t5.87877087384675\t2.93938543692337\t4.81114433617716\t1.74023660764341\t2.76464953963491\t0.00569839814973709\t0.00984268771318224\n-TR1678|c0_g1_i1\t0.738899982352077\t7.85275634721875\t4.29582816478541\t3.12892233414853\t1.14660116223239\t2.72886722708063\t0.00635522860739327\t0.0104999429165628\n-TR4859|c0_g1_i1\t8.91205730249659\t1.28188505334354\t5.09697117792006\t-2.61274053843141\t0.973661400721484\t-2.68341801009608\t0.00728738414676855\t0.0115383582323835\n-TR2672|c0_g1_i1\t22.3129914439134\t7.89947501226409\t15.1062332280887\t-1.45907440'..b'4\t5.78009048085484\t7.46604610022994e-09\t1.89139834539158e-08\n+TR1449|c0_g1_i1\twt_37\twt_ph8\t220.782434528097\t117.26089394399\t169.021664236043\t0.914395516820343\t0.174920034977504\t5.22750591113215\t1.71811907274331e-07\t4.08053279776536e-07\n+TR2278|c0_g1_i1\twt_37\twt_ph8\t594.657329919233\t348.341653317169\t471.499491618201\t0.772496794598277\t0.157892732036131\t4.89254182023719\t9.95419556957436e-07\t2.2250554802578e-06\n+TR5055|c0_g2_i1\twt_37\twt_ph8\t28.6665933385886\t6.05959103586122\t17.3630921872249\t2.18372312866756\t0.505600668447204\t4.31906693354301\t1.5669025864333e-05\t3.30790546024808e-05\n+TR127|c1_g1_i1\twt_37\twt_ph8\t16.3791628279609\t1.58772512712498\t8.98344397754296\t3.22742307122337\t0.758365755070441\t4.25576056097574\t2.08339575851481e-05\t4.16679151702962e-05\n+TR1894|c2_g1_i1\twt_37\twt_ph8\t16.2826445742552\t1.67571344127509\t8.97917900776516\t3.18830464179373\t0.7590595028564\t4.20033558607184\t2.66519649541344e-05\t5.06387334128554e-05\n+TR2672|c0_g1_i1\twt_37\twt_ph8\t22.3129914439134\t7.89947501226409\t15.1062332280887\t1.46563545973546\t0.482353842293509\t3.0385068620302\t0.00237753690029721\t0.00429545997952877\n+TR4859|c0_g1_i1\twt_37\twt_ph8\t8.91205730249659\t1.28188505334354\t5.09697117792006\t2.65126611500267\t0.876469721997014\t3.02493748325022\t0.00248684525130613\t0.00429545997952877\n+TR1678|c0_g1_i1\twt_37\twt_ph8\t0.738899982352077\t7.85275634721875\t4.29582816478541\t-3.18849648433777\t1.0594001628342\t-3.00971870327794\t0.00261489744098202\t0.00432026533727463\n+TR4084|c0_g1_i1\twt_37\twt_ph8\t113.2594381118\t173.837287636503\t143.548362874151\t-0.608939120027998\t0.203268581921877\t-2.99573654851409\t0.00273782859610482\t0.00433489527716597\n+TR3807|c0_g1_i1\twt_37\twt_ph8\t4.23896204531587\t0.352255997713617\t2.29560902151474\t3.15525660545126\t1.31164110647326\t2.4055792319098\t0.0161468501576278\t0.0245432122395943\n+TR3249|c0_g1_i1\twt_37\twt_ph8\t1.36481976577862\t4.37661229401476\t2.87071602989669\t-1.55893212196469\t1.01682768784581\t-1.53313303777885\t0.125243078950272\t0.176625758092245\n+TR1859|c3_g1_i1\twt_37\twt_ph8\t0.361569353912422\t2.25550826604853\t1.30853880998047\t-2.19284922770108\t1.43126836745787\t-1.53210206943641\t0.125497249170806\t0.176625758092245\n+TR2090|c0_g1_i1\twt_37\twt_ph8\t0\t5.87877087384675\t2.93938543692337\t-2.86225136793822\t1.9729684338102\t-1.45073348305458\t0.146854088052773\t0.19930197664305\n+TR1982|c2_g1_i1\twt_37\twt_ph8\t7.00144976454503\t11.520013112092\t9.26073143831853\t-0.712688609925078\t0.555640746749963\t-1.28264281209345\t0.199617243880331\t0.261567423015607\n+TR1837|c2_g1_i1\twt_37\twt_ph8\t0.377330628439655\t1.67813520813222\t1.02773291828594\t-1.7572235261621\t1.52690431775837\t-1.15084062945205\t0.249797806431129\t0.316410554812763\n+TR5212|c0_g1_i1\twt_37\twt_ph8\t80.2050001877881\t94.8352723753388\t87.5201362815635\t-0.23592411895009\t0.215502649097795\t-1.09476203628025\t0.273620902411289\t0.335406267471903\n+TR3854|c0_g1_i1\twt_37\twt_ph8\t1925.26464813324\t2107.16376011081\t2016.21420412203\t-0.130483054839334\t0.130739272627028\t-0.998040238540833\t0.318259846991125\t0.377933568301961\n+TR1122|c0_g1_i1\twt_37\twt_ph8\t1.69354093201913\t0.660517838352177\t1.17702938518565\t1.18649040337028\t1.40558655511286\t0.84412475279761\t0.398599697111289\t0.448776409473292\n+TR2844|c0_g1_i1\twt_37\twt_ph8\t193.030766468894\t213.82243412349\t203.426600296192\t-0.143791883173722\t0.17140940841448\t-0.838879758723761\t0.401536787423471\t0.448776409473292\n+TR2011|c5_g1_i1\twt_37\twt_ph8\t6.84875389533898\t4.81927837273561\t5.8340161340373\t0.467659672901774\t0.714270969980296\t0.654737057162879\t0.512637061952329\t0.556577381548243\n+TR2182|c3_g2_i6\twt_37\twt_ph8\t2.76248771922916\t1.94482465855284\t2.353656188891\t0.479324872360299\t1.02378035563408\t0.468191120998245\t0.639647921157653\t0.675183916777523\n+TR3788|c0_g1_i1\twt_37\twt_ph8\t23.7579432209456\t26.0024682525169\t24.8802057367313\t-0.124358222905796\t0.350105186670918\t-0.355202458119214\t0.72243792333433\t0.741963272613636\n+TR939|c0_g1_i1\twt_37\twt_ph8\t103.002135647151\t102.820214322362\t102.911174984756\t0.000971215955472081\t0.195414642848595\t0.00497002651037041\t0.996034508905975\t0.996034508905975\n' |
| b |
| diff -r 1fc32fd3fb3f -r 8b5039bdf1f6 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix Fri Mar 31 11:37:24 2017 -0400 |
| b |
| @@ -0,0 +1,39 @@ +wt_37_1 wt_37_2 wt_37_3 wt_ph8_1 wt_ph8_2 wt_ph8_3 +TR24|c0_g1_i1 85 90 67 196 201 222 +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 |
| b |
| diff -r 1fc32fd3fb3f -r 8b5039bdf1f6 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.count_matrix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.count_matrix Fri Mar 31 11:37:24 2017 -0400 |
| b |
| @@ -0,0 +1,39 @@ +wt_37_1 wt_37_2 wt_37_3 wt_ph8_1 wt_ph8_2 wt_ph8_3 +TR24|c0_g1_i1 85 90 67 196 201 222 +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 |
| b |
| diff -r 1fc32fd3fb3f -r 8b5039bdf1f6 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.count_matrix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.count_matrix Fri Mar 31 11:37:24 2017 -0400 |
| b |
| @@ -0,0 +1,39 @@ +wt_37_1 wt_37_2 wt_37_3 wt_ph8_1 wt_ph8_2 wt_ph8_3 +TR24|c0_g1_i1 85 90 67 196 201 222 +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 |
| b |
| diff -r 1fc32fd3fb3f -r 8b5039bdf1f6 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results --- a/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results Thu Mar 23 10:18:33 2017 -0400 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results Fri Mar 31 11:37:24 2017 -0400 |
| b |
| b'@@ -1,40 +1,40 @@\n-id\tbaseMeanA\tbaseMeanB\tbaseMean\tlog2FoldChange\tlfcSE\tstat\tpvalue\tpadj\n-TR2779|c0_g1_i1\t195.849684476753\t966.924129135581\t581.386906806167\t2.25621220756415\t0.156114979193812\t14.4522467940961\t2.42639762934434e-47\t5.82335431042642e-46\n-TR1891|c0_g1_i1\t128.246229498835\t343.028289972482\t235.637259735659\t1.40479466067472\t0.104376051709838\t13.4589749052781\t2.72672776456232e-41\t3.27207331747478e-40\n-TR4761|c0_g1_i1\t184.029205648389\t351.782300021135\t267.905752834762\t0.934185686537064\t0.0945413616088594\t9.88123791152932\t5.0208774429335e-23\t4.0167019543468e-22\n-TR24|c0_g1_i1\t39.3724575919554\t183.288101009647\t111.330279300801\t2.11680322693425\t0.240338854880295\t8.80757806717753\t1.27878744153922e-18\t7.67272464923531e-18\n-TR3638|c0_g1_i1\t174.266398355818\t297.555274221606\t235.910836288712\t0.75598517202537\t0.0975355931355663\t7.75086455848598\t9.12689947000201e-15\t3.81892706573808e-14\n-TR2122|c0_g2_i2\t190.673533226329\t328.707071692642\t259.690302459485\t0.782528370953275\t0.101034702024136\t7.74514454218254\t9.54731766434521e-15\t3.81892706573808e-14\n-TR2278|c0_g1_i1\t426.804298570637\t315.99710709695\t371.400702833793\t-0.429046906426044\t0.106511998284025\t-4.02815563822158\t5.62161256784655e-05\t0.000192741002326167\n-TR4084|c0_g1_i1\t115.544575735664\t157.970364768418\t136.757470252041\t0.435378746345168\t0.157905703989027\t2.75720721510747\t0.00582973950434901\t0.017489218513047\n-TR3788|c0_g1_i1\t128.115824993653\t24.010679388938\t76.0632521912957\t-1.20076602288383\t0.555078500739638\t-2.16323640941564\t0.0305230012251409\t0.0813946699337092\n-TR1678|c0_g1_i1\t0.695005959508731\t7.10082184137838\t3.89791390044355\t1.13542782611345\t0.54389306361848\t2.08759387104432\t0.0368344853417399\t1\n-TR1859|c3_g1_i1\t0\t2.05957798928713\t1.02978899464357\t1.08547672488113\t0.52169423531112\t2.08067609609255\t0.0374635634690378\t1\n-TR1479|c0_g1_i1\t353.92669362375\t305.546165789569\t329.736429706659\t-0.210273055725041\t0.101401657889395\t-2.07366487000044\t0.0381104459877385\t0.0914650703705724\n-TR1492|c0_g1_i2\t1368.89238848897\t813.514514376559\t1091.20345143276\t-0.673957173112486\t0.33643480733027\t-2.00323259790084\t0.0451523282811554\t0.0985141707952481\n-TR2844|c0_g1_i1\t220.566338218013\t194.214843050373\t207.390590634193\t-0.1851823349888\t0.101213323108161\t-1.8296240979155\t0.0673061677634479\t0.134612335526896\n-TR5075|c0_g1_i1\t8.81552188359314\t126.23137395943\t67.5234479215117\t0.86620707327725\t0.498591364017662\t1.73730861741634\t0.0823327113057556\t0.151998851641395\n-TR2107|c1_g1_i1\t7.08292121571621\t1.78415791317121\t4.43353956444371\t-0.87765751535477\t0.553196716703176\t-1.58651974759584\t0.112621456124343\t1\n-TR2672|c0_g1_i1\t2.07518941673641\t7.44710458698621\t4.76114700186131\t0.652733502871168\t0.537764458916032\t1.21379070715621\t0.224827655823799\t1\n-TR4859|c0_g1_i1\t3.10763825129944\t1.1806627783491\t2.14415051482427\t-0.587630876626665\t0.551071114588281\t-1.06634309269812\t0.28626857627862\t1\n-TR3091|c0_g1_i1\t312.47018793986\t293.531643106953\t303.000915523406\t-0.0879738435317154\t0.0902971665647824\t-0.97427025540829\t0.329922369379669\t0.501282895914669\n-TR4163|c0_g1_i1\t221.469120691076\t207.118822998308\t214.293971844692\t-0.0959599050588562\t0.0987561344325879\t-0.97168551209707\t0.331207026506115\t0.501282895914669\n-TR4669|c0_g2_i1\t165.630009730314\t0\t82.8150048651569\t-0.322459466822447\t0.333908718519009\t-0.965711432311973\t0.334188597276446\t0.501282895914669\n-TR1894|c2_g1_i1\t2.85762748931802\t1.47338219762144\t2.16550484346973\t-0.426208431542948\t0.551264679640795\t-0.773146634064541\t0.439435604855973\t1\n-TR3249|c0_g1_i1\t2.06512931203634\t4.15451161800812\t3.10982046502223\t0.3941103325595\t0.539435464341514\t0.730597742661558\t0.465024891244583\t1\n-TR5212|c0_g1_i1\t102.736339436612\t86.4452993262187\t94.5908193814151\t-0.222704356323449\t0.346653224187607\t-0.642441324021618\t0.520586675617895\t0.734945894989969\n-TR1122|c0_g1_i1\t1.29006258579706\t0.5946183773076\t0.942340481552333\t-0.302591524122929\t0.512417527863229\t-0.590517512905403\t0.554843748171664\t1\n-TR2011|c5_g1_i1\t7.597917075274\t4.42090354598533\t6.00941031062966\t-0.2467378203'..b'53956444371\t0.951944042839851\t0.540599552522162\t1.76090423752399\t0.0782546125949942\t0.170760316089935\n+TR4669|c0_g2_i1\twt_GSNO\twt_ph8\t165.630009730314\t0\t82.8150048651569\t0.762969565911357\t0.439826422982926\t1.73470607049221\t0.0827928805284532\t0.170760316089935\n+TR2672|c0_g1_i1\twt_GSNO\twt_ph8\t2.07518941673641\t7.44710458698621\t4.76114700186131\t-0.686459125319668\t0.52860452101472\t-1.29862514986048\t0.194072602638997\t0.376729169828641\n+TR4859|c0_g1_i1\twt_GSNO\twt_ph8\t3.10763825129944\t1.1806627783491\t2.14415051482427\t0.593225714064679\t0.537217960853533\t1.10425517628294\t0.269482460872864\t0.494051178266917\n+TR3091|c0_g1_i1\twt_GSNO\twt_ph8\t312.47018793986\t293.531643106953\t303.000915523406\t0.0878939148373507\t0.0878811164283744\t1.00014563320878\t0.317240035048796\t0.536180698490786\n+TR4163|c0_g1_i1\twt_GSNO\twt_ph8\t221.469120691076\t207.118822998308\t214.293971844692\t0.0959413488001967\t0.0974696330347526\t0.984320406397642\t0.324957999085325\t0.536180698490786\n+TR1894|c2_g1_i1\twt_GSNO\twt_ph8\t2.85762748931802\t1.47338219762144\t2.16550484346973\t0.431530486406946\t0.537372709941065\t0.803037590900872\t0.421953007665329\t0.663069012045517\n+TR3249|c0_g1_i1\twt_GSNO\twt_ph8\t2.06512931203634\t4.15451161800812\t3.10982046502223\t-0.38612563978518\t0.523142120053183\t-0.738089373774619\t0.460460140618999\t0.675718500003336\n+TR5212|c0_g1_i1\twt_GSNO\twt_ph8\t102.736339436612\t86.4452993262187\t94.5908193814151\t0.226915890105892\t0.314756340859895\t0.720925556212693\t0.470955318184143\t0.675718500003336\n+TR1122|c0_g1_i1\twt_GSNO\twt_ph8\t1.29006258579706\t0.5946183773076\t0.942340481552333\t0.279366026492593\t0.486443515520964\t0.57430311552905\t0.565762701275693\t1\n+TR2011|c5_g1_i1\twt_GSNO\twt_ph8\t7.597917075274\t4.42090354598533\t6.00941031062966\t0.293830308686626\t0.525066976727929\t0.559605386950241\t0.575748629670957\t0.791654365797565\n+TR1837|c2_g1_i1\twt_GSNO\twt_ph8\t2.16507864525674\t1.46465683073113\t1.81486773799393\t0.232644077202222\t0.530765383353658\t0.438318105322267\t0.661155703054792\t1\n+TR1982|c2_g1_i1\twt_GSNO\twt_ph8\t5.5352448786851\t10.687042573374\t8.11114372602957\t-0.163617497783336\t0.41190705551325\t-0.397219459082736\t0.691205633846634\t0.874699343226649\n+TR1449|c0_g1_i1\twt_GSNO\twt_ph8\t98.9943307118646\t106.843279101242\t102.918804906553\t-0.100378154615576\t0.259464578599584\t-0.38686650469729\t0.69885503944156\t0.874699343226649\n+TR2182|c3_g2_i6\twt_GSNO\twt_ph8\t1.29006258579706\t1.76655578876639\t1.52830918728173\t-0.199699696686908\t0.518464312092113\t-0.385175395932417\t0.700107470922461\t1\n+TR4277|c0_g1_i1\twt_GSNO\twt_ph8\t153.969096204861\t149.159426886469\t151.564261545665\t0.0459499001744168\t0.126145529370448\t0.364261027748966\t0.715663099003622\t0.874699343226649\n+TR3854|c0_g1_i1\twt_GSNO\twt_ph8\t2260.55060252051\t1927.46472630351\t2094.00766441201\t0.149461409336011\t0.515737174792397\t0.289801504799756\t0.771968096584582\t0.909819542403257\n+TR127|c1_g1_i1\twt_GSNO\twt_ph8\t1.20754470361908\t1.49113571265046\t1.34934020813477\t-0.140499936513031\t0.525109891787989\t-0.267562921038549\t0.789035775295455\t1\n+TR2090|c0_g1_i1\twt_GSNO\twt_ph8\t9.46045896251181\t5.6546754787973\t7.55756722065455\t0.0558182109444541\t0.287850208274631\t0.193914089133468\t0.846243151562143\t0.956832805790417\n+TR3807|c0_g1_i1\twt_GSNO\twt_ph8\t0.347502979754365\t0.292870809896544\t0.320186894825454\t0.0816135421729034\t0.465942705668376\t0.175157892118586\t0.860955569985101\t1\n+TR131|c0_g1_i1\twt_GSNO\twt_ph8\t1275.67603302799\t1312.2934796972\t1293.9847563626\t-0.035805337908038\t0.355352253126282\t-0.100760126305753\t0.919740880292126\t0.956832805790417\n+TR5055|c0_g2_i1\twt_GSNO\twt_ph8\t5.17791343714095\t5.60171771495863\t5.38981557604979\t-0.0489219520111245\t0.535247232645477\t-0.091400663146498\t0.927174234841818\t0.956832805790417\n+TR939|c0_g1_i1\twt_GSNO\twt_ph8\t92.2508462008296\t94.0990807885678\t93.1749634946987\t-0.0260132924520656\t0.31360944301959\t-0.0829480522065804\t0.933892845523313\t0.956832805790417\n+TR2487|c0_g1_i1\twt_GSNO\twt_ph8\t875.181494043204\t882.631049341941\t878.906271692572\t-0.0117684251443531\t0.217416529127567\t-0.0541284749212796\t0.956832805790417\t0.956832805790417\n' |
| b |
| diff -r 1fc32fd3fb3f -r 8b5039bdf1f6 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix Fri Mar 31 11:37:24 2017 -0400 |
| b |
| @@ -0,0 +1,40 @@ +wt_GSNO_1 wt_GSNO_2 wt_GSNO_3 wt_ph8_1 wt_ph8_2 wt_ph8_3 +TR24|c0_g1_i1 35 34 36 196 201 222 +TR2779|c0_g1_i1 186 197 147 1094 1086 1088 +TR127|c1_g1_i1 0 1 2 1 1 3 +TR2107|c1_g1_i1 6 7 6 1 2 3 +TR2011|c5_g1_i1 5 7 8 4 8 3 +TR4163|c0_g1_i1 216 210 172 254 212 234 +TR5055|c0_g2_i1 7 3 4 4 11 4 +TR1449|c0_g1_i1 113 91 66 130 107 124 +TR1982|c2_g1_i1 3 8 4 9 11 16 +TR1859|c3_g1_i1 0 0 0 2 4 1 +TR1492|c0_g1_i2 1263 1319 1104 929 922 899 +TR1122|c0_g1_i1 0 0 3 1 0 1 +TR2278|c0_g1_i1 406 413 333 409 337 323 +TR4084|c0_g1_i1 111 127 77 201 158 175 +TR4761|c0_g1_i1 174 165 155 389 406 394 +TR3638|c0_g1_i1 184 174 117 344 338 324 +TR2090|c0_g1_i1 0 0 22 0 9 10 +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 |
| b |
| diff -r 1fc32fd3fb3f -r 8b5039bdf1f6 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.count_matrix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.count_matrix Fri Mar 31 11:37:24 2017 -0400 |
| b |
| @@ -0,0 +1,40 @@ +wt_GSNO_1 wt_GSNO_2 wt_GSNO_3 wt_ph8_1 wt_ph8_2 wt_ph8_3 +TR24|c0_g1_i1 35 34 36 196 201 222 +TR2779|c0_g1_i1 186 197 147 1094 1086 1088 +TR127|c1_g1_i1 0 1 2 1 1 3 +TR2107|c1_g1_i1 6 7 6 1 2 3 +TR2011|c5_g1_i1 5 7 8 4 8 3 +TR4163|c0_g1_i1 216 210 172 254 212 234 +TR5055|c0_g2_i1 7 3 4 4 11 4 +TR1449|c0_g1_i1 113 91 66 130 107 124 +TR1982|c2_g1_i1 3 8 4 9 11 16 +TR1859|c3_g1_i1 0 0 0 2 4 1 +TR1492|c0_g1_i2 1263 1319 1104 929 922 899 +TR1122|c0_g1_i1 0 0 3 1 0 1 +TR2278|c0_g1_i1 406 413 333 409 337 323 +TR4084|c0_g1_i1 111 127 77 201 158 175 +TR4761|c0_g1_i1 174 165 155 389 406 394 +TR3638|c0_g1_i1 184 174 117 344 338 324 +TR2090|c0_g1_i1 0 0 22 0 9 10 +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 |
| b |
| diff -r 1fc32fd3fb3f -r 8b5039bdf1f6 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.count_matrix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.count_matrix Fri Mar 31 11:37:24 2017 -0400 |
| b |
| @@ -0,0 +1,40 @@ +wt_GSNO_1 wt_GSNO_2 wt_GSNO_3 wt_ph8_1 wt_ph8_2 wt_ph8_3 +TR24|c0_g1_i1 35 34 36 196 201 222 +TR2779|c0_g1_i1 186 197 147 1094 1086 1088 +TR127|c1_g1_i1 0 1 2 1 1 3 +TR2107|c1_g1_i1 6 7 6 1 2 3 +TR2011|c5_g1_i1 5 7 8 4 8 3 +TR4163|c0_g1_i1 216 210 172 254 212 234 +TR5055|c0_g2_i1 7 3 4 4 11 4 +TR1449|c0_g1_i1 113 91 66 130 107 124 +TR1982|c2_g1_i1 3 8 4 9 11 16 +TR1859|c3_g1_i1 0 0 0 2 4 1 +TR1492|c0_g1_i2 1263 1319 1104 929 922 899 +TR1122|c0_g1_i1 0 0 3 1 0 1 +TR2278|c0_g1_i1 406 413 333 409 337 323 +TR4084|c0_g1_i1 111 127 77 201 158 175 +TR4761|c0_g1_i1 174 165 155 389 406 394 +TR3638|c0_g1_i1 184 174 117 344 338 324 +TR2090|c0_g1_i1 0 0 22 0 9 10 +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 |
| b |
| diff -r 1fc32fd3fb3f -r 8b5039bdf1f6 test-data/count/trinotate/genes.lengths.txt --- a/test-data/count/trinotate/genes.lengths.txt Thu Mar 23 10:18:33 2017 -0400 +++ b/test-data/count/trinotate/genes.lengths.txt Fri Mar 31 11:37:24 2017 -0400 |
| b |
| @@ -38,3 +38,4 @@ TR1678|c0_g1_i1 221.00 TR3249|c0_g1_i1 221.00 TR1479|c0_g1_i1 136.00 +TR4669|c0_g2_i1 136.00 |
| b |
| diff -r 1fc32fd3fb3f -r 8b5039bdf1f6 test-data/filtered/Trinity_filtered_exp.fasta --- a/test-data/filtered/Trinity_filtered_exp.fasta Thu Mar 23 10:18:33 2017 -0400 +++ b/test-data/filtered/Trinity_filtered_exp.fasta Fri Mar 31 11:37:24 2017 -0400 |
| [ |
| @@ -1,4 +1,4 @@ ->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 +>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT @@ -6,12 +6,12 @@ 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 +>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC ->TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT @@ -22,12 +22,12 @@ CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT G ->TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC ATACATGATTCTATTCAACCAA ->TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA |
| b |
| diff -r 1fc32fd3fb3f -r 8b5039bdf1f6 test-data/filtered/Trinity_filtered_hi_iso.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered/Trinity_filtered_hi_iso.fasta Fri Mar 31 11:37:24 2017 -0400 |
| [ |
| @@ -0,0 +1,45 @@ +>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG +CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC +AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT +ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG +GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG +AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG +TATATGGTACAGATGTAAAG +>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT +TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT +ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA +TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC +>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA +ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC +AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG +AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA +AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA +>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT +TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA +TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT +TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT +AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT +ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA +AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC +CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG +GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT +G +>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA +GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC +TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG +TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC +>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC +AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC +CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC +ATACATGATTCTATTCAACCAA +>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG +CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT +ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA +TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT |
| b |
| diff -r 1fc32fd3fb3f -r 8b5039bdf1f6 tool_dependencies.xml --- a/tool_dependencies.xml Thu Mar 23 10:18:33 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,30 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="trinity" version="2.2.0"> - <repository changeset_revision="76d63b5c571a" name="package_trinity_2_2_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="bowtie" version="1.1.2"> - <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="bowtie2" version="2.2.6"> - <repository changeset_revision="0d9cd7487cc9" name="package_bowtie_2_2_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="bioconductor-edger" version="3.14.0"> - <repository changeset_revision="5f4abad5b2c1" name="package_bioconductor_edger_3_14_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="rsem" version="1.2.28"> - <repository changeset_revision="4567331d510a" name="package_rsem_1_2_28" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="eXpress" version="1.5.1"> - <repository changeset_revision="93017e8743e5" name="package_express_1_5_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="bioconductor-limma" version="3.28.10"> - <repository changeset_revision="b313488c66bd" name="package_bioconductor_limma_3_28_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="deseq2" version="1.10.0"> - <repository changeset_revision="e4a11a7d33d6" name="package_deseq2_1_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <set_environment version="1.0"> - <environment_variable action="set_to" name="TRINITY_MEM_OPTIONS">'--max_memory 30G --bflyHeapSpaceMax 30G'</environment_variable> - </set_environment> -</tool_dependency> |