Mercurial > repos > iuc > trinity
changeset 15:e65e640e6196 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
line wrap: on
line diff
--- a/README.rst Thu Mar 23 10:15:32 2017 -0400 +++ b/README.rst Fri Mar 31 11:35:34 2017 -0400 @@ -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' +
--- a/macros.xml Thu Mar 23 10:15:32 2017 -0400 +++ b/macros.xml Fri Mar 31 11:35:34 2017 -0400 @@ -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>
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results Thu Mar 23 10:15:32 2017 -0400 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results Fri Mar 31 11:35:34 2017 -0400 @@ -1,39 +1,38 @@ -id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj -TR4277|c0_g1_i1 3852.97388871986 161.116814813422 2007.04535176664 -4.57259674791206 0.121601866332754 -37.6030145409076 0 0 -TR131|c0_g1_i1 26.1866396538608 1340.30918254958 683.247911101723 5.67372481552909 0.187406695960058 30.274931140872 2.45144211418965e-201 4.04487948841292e-200 -TR4761|c0_g1_i1 1645.20640957447 193.196157329029 919.201283451752 -3.08847487551254 0.143642016580712 -21.5011940728159 1.51733402752078e-102 1.66906743027286e-101 -TR3091|c0_g1_i1 16.7444693227929 328.569936894811 172.657203108802 4.29039998257063 0.240421038467916 17.8453599980735 3.14072644239509e-71 2.59109931497595e-70 -TR3638|c0_g1_i1 583.00358519031 183.754416330029 383.37900076017 -1.66018915730897 0.144484444213305 -11.4904352945982 1.47367477630653e-30 9.72625352362312e-30 -TR2487|c0_g1_i1 342.210853400436 920.407318992504 631.30908619647 1.42690938766606 0.124693202553469 11.4433614539188 2.5385551583546e-30 1.39620533709503e-29 -TR3788|c0_g1_i1 19.5075441237117 134.95369713876 77.2306206312357 2.77038513264018 0.262760026053246 10.5434040871909 5.44900939296595e-26 2.56881871382681e-25 -TR1479|c0_g1_i1 129.593534475689 371.064629188207 250.329081831948 1.51441163103673 0.145431922863633 10.4131995315551 2.1584296431011e-25 8.90352227779205e-25 -TR2107|c1_g1_i1 48.9228907410258 7.40521775805688 28.1640542495414 -2.6949883047084 0.431525668867458 -6.24525607429428 4.23106352657394e-10 1.55138995974378e-09 -TR3854|c0_g1_i1 1573.69549271337 2374.56159860719 1974.12854566028 0.593513416954248 0.111306645736399 5.33223701987958 9.70102011419466e-08 3.20133663768424e-07 -TR2122|c0_g2_i2 119.534640490118 199.143666337033 159.339153413576 0.738656537188098 0.168436715892782 4.38536534788702 1.15791268060543e-05 3.47373804181628e-05 -TR1449|c0_g1_i1 180.814952011467 104.755290736358 142.785121373912 -0.784194659361461 0.185749133486416 -4.2217944420118 2.42365089281258e-05 6.61949164163031e-05 -TR4163|c0_g1_i1 347.283468916919 232.772947466212 290.028208191566 -0.576744528291395 0.137147958253208 -4.20527243450891 2.60767852549073e-05 6.61949164163031e-05 -TR2672|c0_g1_i1 18.3155337236093 2.26581902751323 10.2906763755613 -2.88818323474529 0.724350842979802 -3.98727117216294 6.68376171815065e-05 0.000157545811927837 -TR127|c1_g1_i1 13.461799216177 1.21881296083961 7.34030608850831 -3.33218181130749 0.914685635912973 -3.64298036448506 0.000269499403689035 0.000576210779000196 -TR5055|c0_g2_i1 23.3590211688541 5.52768338415684 14.4433522765055 -2.04478780320925 0.562727305023446 -3.63370994255211 0.00027937492315161 0.000576210779000196 -TR2844|c0_g1_i1 158.206282615139 231.762548186068 194.984415400603 0.550641897280872 0.154759496937021 3.55804915484414 0.000373619406412113 0.000725261200682336 -TR5212|c0_g1_i1 65.7079302129484 107.875371765755 86.7916509893515 0.713884138135847 0.209708011296715 3.40418152707468 0.000663626354411326 0.00121664831642076 -TR1894|c2_g1_i1 13.3497721959996 2.96749216411516 8.15863218005739 -2.04982326482473 0.714661961266818 -2.8682417365424 0.00412760030232129 0.00716898999876856 -TR24|c0_g1_i1 69.9065207344592 41.2394742844514 55.5729975094553 -0.760369639593845 0.269117661787534 -2.8254170853868 0.00472191070589177 0.00779115266472142 -TR4669|c0_g2_i1 0 167.096667347181 83.5483336735905 4.37844609928899 2.00484514683835 2.18393231327309 0.0289672221614669 0.0455199205394479 -TR2779|c0_g1_i1 155.915506826481 205.619872596257 180.767689711369 0.402360429872658 0.188906223389576 2.12994798505331 0.0331759079102528 0.0497638618653791 -TR1492|c0_g1_i2 1640.89375005483 1435.64893261411 1538.27134133447 -0.192484740220531 0.101376439014472 -1.89871277874588 0.0576022504671541 0.0796285639028554 -TR3807|c0_g1_i1 3.48709246029019 0.350050334268211 1.9185713972792 -2.70461238638113 1.4262081182078 -1.89636586123194 0.0579116828384403 0.0796285639028554 -TR4084|c0_g1_i1 93.2264707954139 121.352438036668 107.289454416041 0.3802042378315 0.213056828958299 1.78452030704877 0.0743391580521785 0.0981276886288757 -TR1891|c0_g1_i1 107.628573623499 135.399287466928 121.513930545214 0.328806752550927 0.189034600977243 1.73939982866159 0.0819644583677276 0.104031812543654 -TR1837|c2_g1_i1 0.308903905435236 2.22601224010275 1.26745807276899 2.42365647560727 1.53486167088074 1.57907160077593 0.114319634794044 1 -TR5075|c0_g1_i1 15.8633018853512 9.23822794034992 12.5507649128506 -0.764079585128418 0.506894456921462 -1.50737411840904 0.131714788977897 0.158065100778825 -TR4859|c0_g1_i1 7.32690480813971 3.17910584569163 5.25300532691567 -1.18284590433612 0.789581441931072 -1.49806700299749 0.134115843085064 0.158065100778825 -TR939|c0_g1_i1 84.2568220960088 96.9171174594069 90.5869697777078 0.202696971338398 0.202184598546511 1.00253418309589 0.316085665578007 0.354180332604713 -TR2278|c0_g1_i1 486.5272515724 448.140178813055 467.333715192727 -0.118822731208233 0.119975347874694 -0.990392887481645 0.321982120549739 0.354180332604713 -TR2011|c5_g1_i1 5.60408627995835 7.88255079488408 6.74331853742122 0.488779860259128 0.689341019893534 0.70905378637502 0.478291099766969 0.509148590074515 -TR2182|c3_g2_i6 2.24974854180929 1.3031439398571 1.77644624083319 -0.780861388045469 1.28191780274725 -0.609135302101293 0.54243475986365 0.559385846109389 -TR3249|c0_g1_i1 1.12573841927462 2.128954842887 1.62734663108081 0.761533075632955 1.28978972955114 0.590431958159547 0.554901090261946 1 -TR1678|c0_g1_i1 0.595141051681226 0.700100668536423 0.647620860108824 0.247986780508542 1.73527723872539 0.142909026277954 0.886362029808798 1 -TR1122|c0_g1_i1 1.41370386226057 1.3031439398571 1.35842390105883 -0.16283641618004 1.43170451886811 -0.113736049606644 0.909447034479058 1 -TR1982|c2_g1_i1 5.73684100209948 5.71221669652109 5.72452884931028 0.0102126833240523 0.713573951255734 0.0143120181252136 0.988581051536513 0.988581051536513 -TR2090|c0_g1_i1 0 9.55638889228537 4.77819444614269 3.06235120305875 2.04796345977052 1.49531535264887 NA 1 +sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj +TR4277|c0_g1_i1 wt_37 wt_GSNO 3852.97388871986 161.116814813422 2007.04535176664 4.57260002898197 0.121471586836965 37.6433711623376 0 0 +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 +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 +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 +TR3638|c0_g1_i1 wt_37 wt_GSNO 583.00358519031 183.754416330029 383.37900076017 1.66018954854466 0.144513974558734 11.4880900176883 1.51422805973163e-30 1.12052876420141e-29 +TR2487|c0_g1_i1 wt_37 wt_GSNO 342.210853400436 920.407318992504 631.30908619647 -1.42691086642688 0.124648977132644 -11.4474334186348 2.42211055832184e-30 1.49363484429847e-29 +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 +TR1479|c0_g1_i1 wt_37 wt_GSNO 129.593534475689 371.064629188207 250.329081831948 -1.51441062491813 0.145530800926874 -10.4061175728641 2.32511621828936e-25 1.07536625095883e-24 +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 +TR3854|c0_g1_i1 wt_37 wt_GSNO 1573.69549271337 2374.56159860719 1974.12854566028 -0.593515573382884 0.111170659243154 -5.33877893163104 9.35746583039244e-08 3.4622623572452e-07 +TR2122|c0_g2_i2 wt_37 wt_GSNO 119.534640490118 199.143666337033 159.339153413576 -0.738644008220832 0.168659021315898 -4.37951081690053 1.18946017688789e-05 4.00091150407745e-05 +TR1449|c0_g1_i1 wt_37 wt_GSNO 180.814952011467 104.755290736358 142.785121373912 0.784193680180578 0.186004942516637 4.21598302480827 2.48692468039376e-05 7.49709472786912e-05 +TR4163|c0_g1_i1 wt_37 wt_GSNO 347.283468916919 232.772947466212 290.028208191566 0.576743600823335 0.13722219355458 4.20299068163444 2.63411436384591e-05 7.49709472786912e-05 +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 +TR127|c1_g1_i1 wt_37 wt_GSNO 13.461799216177 1.21881296083961 7.34030608850831 3.33150202228086 0.915899815581865 3.63740877070095 0.000275394687501815 0.000667511143840185 +TR5055|c0_g2_i1 wt_37 wt_GSNO 23.3590211688541 5.52768338415684 14.4433522765055 2.04460941512382 0.563987307210913 3.62527558507482 0.000288653467606567 0.000667511143840185 +TR2844|c0_g1_i1 wt_37 wt_GSNO 158.206282615139 231.762548186068 194.984415400603 -0.550639207704626 0.154913717539885 -3.55448966333699 0.000378713397971402 0.000824258572055403 +TR5212|c0_g1_i1 wt_37 wt_GSNO 65.7079302129484 107.875371765755 86.7916509893515 -0.713874873222434 0.210087143945163 -3.39799408862815 0.000678818868686303 0.00139534989674407 +TR1894|c2_g1_i1 wt_37 wt_GSNO 13.3497721959996 2.96749216411516 8.15863218005739 2.04972102673103 0.716146945354672 2.86215146210796 0.00420775772107294 0.00819405450945783 +TR24|c0_g1_i1 wt_37 wt_GSNO 69.9065207344592 41.2394742844514 55.5729975094553 0.760351613917761 0.269735390145923 2.81887969356346 0.00481915767774413 0.00891544170382664 +TR2779|c0_g1_i1 wt_37 wt_GSNO 155.915506826481 205.619872596257 180.767689711369 -0.402350189521528 0.18910416680051 -2.12766432558821 0.0333649247395808 0.0587858197792614 +TR3807|c0_g1_i1 wt_37 wt_GSNO 3.48709246029019 0.350050334268211 1.9185713972792 2.6523001983829 1.38324824664578 1.91744338358239 0.055181627150862 0.092164962039527 +TR1492|c0_g1_i2 wt_37 wt_GSNO 1640.89375005483 1435.64893261411 1538.27134133447 0.192484568368337 0.101250195527162 1.90107848548993 0.057291733159706 0.092164962039527 +TR4084|c0_g1_i1 wt_37 wt_GSNO 93.2264707954139 121.352438036668 107.289454416041 -0.380198430346905 0.213412163689062 -1.78152183912463 0.0748272403991533 0.115358662282028 +TR1891|c0_g1_i1 wt_37 wt_GSNO 107.628573623499 135.399287466928 121.513930545214 -0.328810062058933 0.189329296532127 -1.73670989161013 0.0824383909023624 0.122008818535496 +TR4669|c0_g2_i1 wt_37 wt_GSNO 0 167.096667347181 83.5483336735905 -3.46077834317638 2.04233842282563 -1.69451757088734 0.0901669757000038 0.128314542342313 +TR1837|c2_g1_i1 wt_37 wt_GSNO 0.308903905435236 2.22601224010275 1.26745807276899 -2.41951712666755 1.51166579847997 -1.60056351681732 0.1094736282342 0.150019416469089 +TR5075|c0_g1_i1 wt_37 wt_GSNO 15.8633018853512 9.23822794034992 12.5507649128506 0.764028730403883 0.508108615055784 1.50367206491864 0.132665825459353 0.172493073735055 +TR4859|c0_g1_i1 wt_37 wt_GSNO 7.32690480813971 3.17910584569163 5.25300532691567 1.18248087647214 0.791530422232021 1.49391715499409 0.135197274008557 0.172493073735055 +TR939|c0_g1_i1 wt_37 wt_GSNO 84.2568220960088 96.9171174594069 90.5869697777078 -0.202690605185084 0.202556787736977 -1.00066064163834 0.316990901598642 0.384256032989688 +TR2278|c0_g1_i1 wt_37 wt_GSNO 486.5272515724 448.140178813055 467.333715192727 0.118822806572317 0.119966033346418 0.99047041281427 0.321944243856225 0.384256032989688 +TR2011|c5_g1_i1 wt_37 wt_GSNO 5.60408627995835 7.88255079488408 6.74331853742122 -0.48861876789566 0.691406970296359 -0.706702114510391 0.479751615248569 0.554712805131158 +TR2182|c3_g2_i6 wt_37 wt_GSNO 2.24974854180929 1.3031439398571 1.77644624083319 0.779605221657958 1.28583289420755 0.606303684693354 0.544313112275579 0.605163179078445 +TR3249|c0_g1_i1 wt_37 wt_GSNO 1.12573841927462 2.128954842887 1.62734663108081 -0.761341397480685 1.29336792501876 -0.58865028485196 0.556095894288301 0.605163179078445 +TR1678|c0_g1_i1 wt_37 wt_GSNO 0.595141051681226 0.700100668536423 0.647620860108824 -0.247288262290953 1.73789746083653 -0.14229162989393 0.886849657633351 0.935371730620685 +TR1122|c0_g1_i1 wt_37 wt_GSNO 1.41370386226057 1.3031439398571 1.35842390105883 0.162148276801819 1.43591594510694 0.112923237153511 0.910091413576882 0.935371730620685 +TR1982|c2_g1_i1 wt_37 wt_GSNO 5.73684100209948 5.71221669652109 5.72452884931028 -0.0101267142582557 0.715373046105777 -0.0141558510114153 0.988705642243408 0.988705642243408
--- /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 11:35:34 2017 -0400 @@ -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.count_matrix Fri Mar 31 11:35:34 2017 -0400 @@ -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.count_matrix Fri Mar 31 11:35:34 2017 -0400 @@ -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
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results Thu Mar 23 10:15:32 2017 -0400 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results Fri Mar 31 11:35:34 2017 -0400 @@ -1,39 +1,39 @@ -id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj -TR4277|c0_g1_i1 4705.34614971641 162.902721493704 2434.12443560506 -4.84860951090545 0.124597307945428 -38.9142397284305 0 0 -TR131|c0_g1_i1 32.0461070493257 1436.30905989883 734.177583474076 5.48367743370229 0.196017912869615 27.9753893581648 3.23827538807456e-172 6.15272323734167e-171 -TR4761|c0_g1_i1 2012.6141923276 384.620292965437 1198.61724264652 -2.38450946693381 0.143863830576436 -16.5747669680385 1.06073316501088e-61 1.34359534234711e-60 -TR3091|c0_g1_i1 20.4914097091341 321.651020117047 171.071214913091 3.96886910507283 0.256323110469072 15.4838519937191 4.45952081812589e-54 4.2365447772196e-53 -TR2779|c0_g1_i1 191.51955185349 1058.15934185376 624.839446853626 2.46616535412611 0.177102083131526 13.9251064161374 4.4587691300744e-44 3.38866453885655e-43 -TR1492|c0_g1_i2 2006.11782336441 890.823502721036 1448.47066304272 -1.17029110983798 0.12207086547883 -9.58698134274255 9.06997941755552e-22 5.74432029778516e-21 -TR5075|c0_g1_i1 19.3833722195684 136.98672801182 78.1850501156942 2.80049241151413 0.293976352213923 9.52625063350759 1.63066468983638e-21 8.85217974482605e-21 -TR1891|c0_g1_i1 131.416087212132 376.595292171713 254.005689691923 1.51493508389526 0.17090866237033 8.86400409952692 7.71909159725621e-19 3.6665685086967e-18 -TR2487|c0_g1_i1 418.818667162757 965.862817209246 692.340742186001 1.20547893236143 0.136832960243688 8.80985787499278 1.25304626500959e-18 5.29063978559604e-18 -TR3638|c0_g1_i1 713.131183384274 326.063958913919 519.597571149096 -1.1281436752687 0.141731779309567 -7.95970868893582 1.72444792020844e-15 6.55290209679206e-15 -TR2107|c1_g1_i1 59.5986596731862 1.89840873462066 30.7485342039034 -4.81058600791914 0.641850436461167 -7.49487066557473 6.63637683134955e-14 2.29256654173894e-13 -TR2122|c0_g2_i2 146.135958637131 360.821667264163 253.478812950647 1.30334955915215 0.177300500792357 7.35107658087526 1.96616724778278e-13 6.22619628464548e-13 -TR1479|c0_g1_i1 158.005105094407 334.827472148091 246.416288621249 1.07882286721986 0.173458235018578 6.2194963940704 4.98753084614221e-10 1.45789363194926e-09 -TR24|c0_g1_i1 85.6614643869141 199.923709280262 142.792586833588 1.22623657127381 0.213504266341901 5.74338205172044 9.2804014146814e-09 2.51896609827067e-08 -TR4163|c0_g1_i1 424.593720981574 227.471218917767 326.03246994967 -0.900786056392834 0.160721595544993 -5.60463609969988 2.08692952426197e-08 5.28688812813031e-08 -TR2278|c0_g1_i1 594.657329919233 348.341653317169 471.499491618201 -0.772446091346236 0.159105007190944 -4.85494520244241 1.20420038267752e-06 2.79113819122931e-06 -TR1449|c0_g1_i1 220.782434528097 117.26089394399 169.021664236043 -0.913694497348233 0.188477876305836 -4.84775462911953 1.24866708554995e-06 2.79113819122931e-06 -TR127|c1_g1_i1 16.3791628279609 1.58772512712498 8.98344397754296 -3.19771077466237 0.834376974262452 -3.83245328346816 0.00012687169720824 0.000267840249661839 -TR1894|c2_g1_i1 16.2826445742552 1.67571344127509 8.97917900776516 -3.15659686337855 0.834779400611257 -3.7813545244015 0.00015597736029041 0.000307529893573321 -TR5055|c0_g2_i1 28.6665933385886 6.05959103586122 17.3630921872249 -2.17768048931004 0.577307428800381 -3.77213314894485 0.000161857838722801 0.000307529893573321 -TR4084|c0_g1_i1 113.2594381118 173.837287636503 143.548362874151 0.609755827935052 0.219803235717165 2.7740985065373 0.00553549140639085 0.00984268771318224 -TR2090|c0_g1_i1 0 5.87877087384675 2.93938543692337 4.81114433617716 1.74023660764341 2.76464953963491 0.00569839814973709 0.00984268771318224 -TR1678|c0_g1_i1 0.738899982352077 7.85275634721875 4.29582816478541 3.12892233414853 1.14660116223239 2.72886722708063 0.00635522860739327 0.0104999429165628 -TR4859|c0_g1_i1 8.91205730249659 1.28188505334354 5.09697117792006 -2.61274053843141 0.973661400721484 -2.68341801009608 0.00728738414676855 0.0115383582323835 -TR2672|c0_g1_i1 22.3129914439134 7.89947501226409 15.1062332280887 -1.45907440559266 0.562189545530202 -2.59534247335852 0.0094496708578661 0.0143634997039565 -TR3807|c0_g1_i1 4.23896204531587 0.352255997713617 2.29560902151474 -3.05008419968594 1.43726100452922 -2.12215052803511 0.0338250994349076 0.0494366837894803 -TR3249|c0_g1_i1 1.36481976577862 4.37661229401476 2.87071602989669 1.51948727816201 1.15409756308282 1.31660210260141 0.187972033660362 0.255148785128113 -TR1859|c3_g1_i1 0.361569353912422 2.25550826604853 1.30853880998047 2.09887277242766 1.59427549709957 1.31650569568817 0.188004367989136 0.255148785128113 -TR1982|c2_g1_i1 7.00144976454503 11.520013112092 9.26073143831853 0.70490953188932 0.647715898283926 1.0883004937148 0.276462472665158 0.362261171078483 -TR3854|c0_g1_i1 1925.26464813324 2107.16376011081 2016.21420412203 0.130534071096341 0.124633726123269 1.04734147936199 0.29494211171073 0.373593341500258 -TR5212|c0_g1_i1 80.2050001877881 94.8352723753388 87.5201362815635 0.236773654582184 0.240888724170321 0.982917134862537 0.325648223857982 0.399181693761397 -TR1837|c2_g1_i1 0.377330628439655 1.67813520813222 1.02773291828594 1.63744709452968 1.70484764845029 0.960465350682869 0.336821061516539 0.39997501055089 -TR2844|c0_g1_i1 193.030766468894 213.82243412349 203.426600296192 0.144163413939115 0.182129405153131 0.791543868591151 0.428626687374099 0.493570124855023 -TR1122|c0_g1_i1 1.69354093201913 0.660517838352177 1.17702938518565 -1.10951489814723 1.57444243758247 -0.704703374135971 0.48099485111646 0.537582480659573 -TR2011|c5_g1_i1 6.84875389533898 4.81927837273561 5.8340161340373 -0.467994718304978 0.83497566164615 -0.560489053516039 0.575145904101733 0.62444412445331 -TR2182|c3_g2_i6 2.76248771922916 1.94482465855284 2.353656188891 -0.463555959442342 1.17585679724627 -0.394228243207794 0.69341253558072 0.731935454224094 -TR3788|c0_g1_i1 23.7579432209456 26.0024682525169 24.8802057367313 0.125242792795277 0.407913046833573 0.307033064442226 0.75881820512208 0.779326805260514 -TR939|c0_g1_i1 103.002135647151 102.820214322362 102.911174984756 -0.00127076378479059 0.216917077821033 -0.00585829293643274 0.995325785249569 0.995325785249569 +sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj +TR4277|c0_g1_i1 wt_37 wt_ph8 4705.34614971641 162.902721493704 2434.12443560506 4.84804012036106 0.130783542648097 37.0691909868646 8.81406568413535e-301 3.34934495997143e-299 +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 +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 +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 +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 +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 +TR1891|c0_g1_i1 wt_37 wt_ph8 131.416087212132 376.595292171713 254.005689691923 -1.51504907455703 0.163541333568612 -9.26401320997792 1.96889433896152e-20 1.06882835543625e-19 +TR1492|c0_g1_i2 wt_37 wt_ph8 2006.11782336441 890.823502721036 1448.47066304272 1.17018000582475 0.127273970398445 9.19418167093695 3.77859650812701e-20 1.79483334136033e-19 +TR2487|c0_g1_i1 wt_37 wt_ph8 418.818667162757 965.862817209246 692.340742186001 -1.2054117169244 0.138501088570193 -8.70326529104133 3.22468912161225e-18 1.36153540690295e-17 +TR3638|c0_g1_i1 wt_37 wt_ph8 713.131183384274 326.063958913919 519.597571149096 1.12815426477841 0.141332330235517 7.98228022490288 1.43654437320665e-15 5.45886861818526e-15 +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 +TR2122|c0_g2_i2 wt_37 wt_ph8 146.135958637131 360.821667264163 253.478812950647 -1.30371385707787 0.169650604759161 -7.68469914344628 1.53356953387865e-14 4.85630352394907e-14 +TR1479|c0_g1_i1 wt_37 wt_ph8 158.005105094407 334.827472148091 246.416288621249 -1.0787542477693 0.165556938369539 -6.51591083039607 7.22498877976404e-11 2.1119197971618e-10 +TR24|c0_g1_i1 wt_37 wt_ph8 85.6614643869141 199.923709280262 142.792586833588 -1.2279226670979 0.196562275775691 -6.24699048814003 4.18436531652641e-10 1.13575630020003e-09 +TR4163|c0_g1_i1 wt_37 wt_ph8 424.593720981574 227.471218917767 326.03246994967 0.900981410818221 0.155876696706134 5.78009048085484 7.46604610022994e-09 1.89139834539158e-08 +TR1449|c0_g1_i1 wt_37 wt_ph8 220.782434528097 117.26089394399 169.021664236043 0.914395516820343 0.174920034977504 5.22750591113215 1.71811907274331e-07 4.08053279776536e-07 +TR2278|c0_g1_i1 wt_37 wt_ph8 594.657329919233 348.341653317169 471.499491618201 0.772496794598277 0.157892732036131 4.89254182023719 9.95419556957436e-07 2.2250554802578e-06 +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 +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 +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 +TR2672|c0_g1_i1 wt_37 wt_ph8 22.3129914439134 7.89947501226409 15.1062332280887 1.46563545973546 0.482353842293509 3.0385068620302 0.00237753690029721 0.00429545997952877 +TR4859|c0_g1_i1 wt_37 wt_ph8 8.91205730249659 1.28188505334354 5.09697117792006 2.65126611500267 0.876469721997014 3.02493748325022 0.00248684525130613 0.00429545997952877 +TR1678|c0_g1_i1 wt_37 wt_ph8 0.738899982352077 7.85275634721875 4.29582816478541 -3.18849648433777 1.0594001628342 -3.00971870327794 0.00261489744098202 0.00432026533727463 +TR4084|c0_g1_i1 wt_37 wt_ph8 113.2594381118 173.837287636503 143.548362874151 -0.608939120027998 0.203268581921877 -2.99573654851409 0.00273782859610482 0.00433489527716597 +TR3807|c0_g1_i1 wt_37 wt_ph8 4.23896204531587 0.352255997713617 2.29560902151474 3.15525660545126 1.31164110647326 2.4055792319098 0.0161468501576278 0.0245432122395943 +TR3249|c0_g1_i1 wt_37 wt_ph8 1.36481976577862 4.37661229401476 2.87071602989669 -1.55893212196469 1.01682768784581 -1.53313303777885 0.125243078950272 0.176625758092245 +TR1859|c3_g1_i1 wt_37 wt_ph8 0.361569353912422 2.25550826604853 1.30853880998047 -2.19284922770108 1.43126836745787 -1.53210206943641 0.125497249170806 0.176625758092245 +TR2090|c0_g1_i1 wt_37 wt_ph8 0 5.87877087384675 2.93938543692337 -2.86225136793822 1.9729684338102 -1.45073348305458 0.146854088052773 0.19930197664305 +TR1982|c2_g1_i1 wt_37 wt_ph8 7.00144976454503 11.520013112092 9.26073143831853 -0.712688609925078 0.555640746749963 -1.28264281209345 0.199617243880331 0.261567423015607 +TR1837|c2_g1_i1 wt_37 wt_ph8 0.377330628439655 1.67813520813222 1.02773291828594 -1.7572235261621 1.52690431775837 -1.15084062945205 0.249797806431129 0.316410554812763 +TR5212|c0_g1_i1 wt_37 wt_ph8 80.2050001877881 94.8352723753388 87.5201362815635 -0.23592411895009 0.215502649097795 -1.09476203628025 0.273620902411289 0.335406267471903 +TR3854|c0_g1_i1 wt_37 wt_ph8 1925.26464813324 2107.16376011081 2016.21420412203 -0.130483054839334 0.130739272627028 -0.998040238540833 0.318259846991125 0.377933568301961 +TR1122|c0_g1_i1 wt_37 wt_ph8 1.69354093201913 0.660517838352177 1.17702938518565 1.18649040337028 1.40558655511286 0.84412475279761 0.398599697111289 0.448776409473292 +TR2844|c0_g1_i1 wt_37 wt_ph8 193.030766468894 213.82243412349 203.426600296192 -0.143791883173722 0.17140940841448 -0.838879758723761 0.401536787423471 0.448776409473292 +TR2011|c5_g1_i1 wt_37 wt_ph8 6.84875389533898 4.81927837273561 5.8340161340373 0.467659672901774 0.714270969980296 0.654737057162879 0.512637061952329 0.556577381548243 +TR2182|c3_g2_i6 wt_37 wt_ph8 2.76248771922916 1.94482465855284 2.353656188891 0.479324872360299 1.02378035563408 0.468191120998245 0.639647921157653 0.675183916777523 +TR3788|c0_g1_i1 wt_37 wt_ph8 23.7579432209456 26.0024682525169 24.8802057367313 -0.124358222905796 0.350105186670918 -0.355202458119214 0.72243792333433 0.741963272613636 +TR939|c0_g1_i1 wt_37 wt_ph8 103.002135647151 102.820214322362 102.911174984756 0.000971215955472081 0.195414642848595 0.00497002651037041 0.996034508905975 0.996034508905975
--- /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 11:35:34 2017 -0400 @@ -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.count_matrix Fri Mar 31 11:35:34 2017 -0400 @@ -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.count_matrix Fri Mar 31 11:35:34 2017 -0400 @@ -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
--- a/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results Thu Mar 23 10:15:32 2017 -0400 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results Fri Mar 31 11:35:34 2017 -0400 @@ -1,40 +1,40 @@ -id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj -TR2779|c0_g1_i1 195.849684476753 966.924129135581 581.386906806167 2.25621220756415 0.156114979193812 14.4522467940961 2.42639762934434e-47 5.82335431042642e-46 -TR1891|c0_g1_i1 128.246229498835 343.028289972482 235.637259735659 1.40479466067472 0.104376051709838 13.4589749052781 2.72672776456232e-41 3.27207331747478e-40 -TR4761|c0_g1_i1 184.029205648389 351.782300021135 267.905752834762 0.934185686537064 0.0945413616088594 9.88123791152932 5.0208774429335e-23 4.0167019543468e-22 -TR24|c0_g1_i1 39.3724575919554 183.288101009647 111.330279300801 2.11680322693425 0.240338854880295 8.80757806717753 1.27878744153922e-18 7.67272464923531e-18 -TR3638|c0_g1_i1 174.266398355818 297.555274221606 235.910836288712 0.75598517202537 0.0975355931355663 7.75086455848598 9.12689947000201e-15 3.81892706573808e-14 -TR2122|c0_g2_i2 190.673533226329 328.707071692642 259.690302459485 0.782528370953275 0.101034702024136 7.74514454218254 9.54731766434521e-15 3.81892706573808e-14 -TR2278|c0_g1_i1 426.804298570637 315.99710709695 371.400702833793 -0.429046906426044 0.106511998284025 -4.02815563822158 5.62161256784655e-05 0.000192741002326167 -TR4084|c0_g1_i1 115.544575735664 157.970364768418 136.757470252041 0.435378746345168 0.157905703989027 2.75720721510747 0.00582973950434901 0.017489218513047 -TR3788|c0_g1_i1 128.115824993653 24.010679388938 76.0632521912957 -1.20076602288383 0.555078500739638 -2.16323640941564 0.0305230012251409 0.0813946699337092 -TR1678|c0_g1_i1 0.695005959508731 7.10082184137838 3.89791390044355 1.13542782611345 0.54389306361848 2.08759387104432 0.0368344853417399 1 -TR1859|c3_g1_i1 0 2.05957798928713 1.02978899464357 1.08547672488113 0.52169423531112 2.08067609609255 0.0374635634690378 1 -TR1479|c0_g1_i1 353.92669362375 305.546165789569 329.736429706659 -0.210273055725041 0.101401657889395 -2.07366487000044 0.0381104459877385 0.0914650703705724 -TR1492|c0_g1_i2 1368.89238848897 813.514514376559 1091.20345143276 -0.673957173112486 0.33643480733027 -2.00323259790084 0.0451523282811554 0.0985141707952481 -TR2844|c0_g1_i1 220.566338218013 194.214843050373 207.390590634193 -0.1851823349888 0.101213323108161 -1.8296240979155 0.0673061677634479 0.134612335526896 -TR5075|c0_g1_i1 8.81552188359314 126.23137395943 67.5234479215117 0.86620707327725 0.498591364017662 1.73730861741634 0.0823327113057556 0.151998851641395 -TR2107|c1_g1_i1 7.08292121571621 1.78415791317121 4.43353956444371 -0.87765751535477 0.553196716703176 -1.58651974759584 0.112621456124343 1 -TR2672|c0_g1_i1 2.07518941673641 7.44710458698621 4.76114700186131 0.652733502871168 0.537764458916032 1.21379070715621 0.224827655823799 1 -TR4859|c0_g1_i1 3.10763825129944 1.1806627783491 2.14415051482427 -0.587630876626665 0.551071114588281 -1.06634309269812 0.28626857627862 1 -TR3091|c0_g1_i1 312.47018793986 293.531643106953 303.000915523406 -0.0879738435317154 0.0902971665647824 -0.97427025540829 0.329922369379669 0.501282895914669 -TR4163|c0_g1_i1 221.469120691076 207.118822998308 214.293971844692 -0.0959599050588562 0.0987561344325879 -0.97168551209707 0.331207026506115 0.501282895914669 -TR4669|c0_g2_i1 165.630009730314 0 82.8150048651569 -0.322459466822447 0.333908718519009 -0.965711432311973 0.334188597276446 0.501282895914669 -TR1894|c2_g1_i1 2.85762748931802 1.47338219762144 2.16550484346973 -0.426208431542948 0.551264679640795 -0.773146634064541 0.439435604855973 1 -TR3249|c0_g1_i1 2.06512931203634 4.15451161800812 3.10982046502223 0.3941103325595 0.539435464341514 0.730597742661558 0.465024891244583 1 -TR5212|c0_g1_i1 102.736339436612 86.4452993262187 94.5908193814151 -0.222704356323449 0.346653224187607 -0.642441324021618 0.520586675617895 0.734945894989969 -TR1122|c0_g1_i1 1.29006258579706 0.5946183773076 0.942340481552333 -0.302591524122929 0.512417527863229 -0.590517512905403 0.554843748171664 1 -TR2011|c5_g1_i1 7.597917075274 4.42090354598533 6.00941031062966 -0.246737820349972 0.517913150509813 -0.476407714511773 0.633783939711306 1 -TR1837|c2_g1_i1 2.16507864525674 1.46465683073113 1.81486773799393 -0.235474161889615 0.546181064177423 -0.431128388246582 0.666375020163124 1 -TR2182|c3_g2_i6 1.29006258579706 1.76655578876639 1.52830918728173 0.209843639881372 0.537581597903129 0.390347513195914 0.696279593847798 1 -TR1449|c0_g1_i1 98.9943307118646 106.843279101242 102.918804906553 0.100194141469895 0.276715374273995 0.362083753867198 0.717289443676285 0.9108498942696 -TR4277|c0_g1_i1 153.969096204861 149.159426886469 151.564261545665 -0.0459267760105497 0.128823197370029 -0.356510139075578 0.721458560376159 0.9108498942696 -TR1982|c2_g1_i1 5.5352448786851 10.687042573374 8.11114372602957 0.110416157924497 0.359967068804195 0.306739608962835 0.759041578558 0.9108498942696 -TR127|c1_g1_i1 1.20754470361908 1.49113571265046 1.34934020813477 0.142968860758062 0.541343527667515 0.26410006484066 0.791702813929264 1 -TR3854|c0_g1_i1 2260.55060252051 1927.46472630351 2094.00766441201 -0.135348942475858 0.546438760787258 -0.247692792291784 0.804372109047297 0.919282410339768 -TR2090|c0_g1_i1 9.46045896251181 5.6546754787973 7.55756722065455 -0.0586395744056909 0.302337767579782 -0.193953851267414 0.846212017000596 1 -TR3807|c0_g1_i1 0.347502979754365 0.292870809896544 0.320186894825454 -0.0640837282416973 0.445995787050203 -0.143686846608001 0.885747758296628 1 -TR131|c0_g1_i1 1275.67603302799 1312.2934796972 1293.9847563626 0.0343724958045096 0.405262489992082 0.0848153891695754 0.932408158838271 0.963782835492881 -TR5055|c0_g2_i1 5.17791343714095 5.60171771495863 5.38981557604979 0.043552763660028 0.53975688204026 0.0806895939805349 0.935688812631814 1 -TR939|c0_g1_i1 92.2508462008296 94.0990807885678 93.1749634946987 0.0253693962827489 0.353966153466169 0.0716718139130601 0.942863087697354 0.963782835492881 -TR2487|c0_g1_i1 875.181494043204 882.631049341941 878.906271692572 0.0115839334384507 0.255112918612705 0.0454070828770402 0.963782835492881 0.963782835492881 +sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj +TR2779|c0_g1_i1 wt_GSNO wt_ph8 195.849684476753 966.924129135581 581.386906806167 -2.26327524632747 0.139880929176731 -16.1800129556472 6.97797522934818e-59 2.3027318256849e-57 +TR1891|c0_g1_i1 wt_GSNO wt_ph8 128.246229498835 343.028289972482 235.637259735659 -1.40437008666625 0.103208263182426 -13.6071477550587 3.63141533276091e-42 5.99183529905551e-41 +TR4761|c0_g1_i1 wt_GSNO wt_ph8 184.029205648389 351.782300021135 267.905752834762 -0.934295661860181 0.0925945355062913 -10.0901814210915 6.10565695161207e-24 6.71622264677328e-23 +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 +TR3638|c0_g1_i1 wt_GSNO wt_ph8 174.266398355818 297.555274221606 235.910836288712 -0.755625651268871 0.0961172743232099 -7.86149687024996 3.79569918101421e-15 2.50516145946938e-14 +TR2122|c0_g2_i2 wt_GSNO wt_ph8 190.673533226329 328.707071692642 259.690302459485 -0.781951344246178 0.102125767694546 -7.65674875105918 1.90699193392882e-14 1.04884556366085e-13 +TR2278|c0_g1_i1 wt_GSNO wt_ph8 426.804298570637 315.99710709695 371.400702833793 0.428907012124225 0.105320470989525 4.07239929801383 4.65313200258197e-05 0.000219361937264579 +TR4084|c0_g1_i1 wt_GSNO wt_ph8 115.544575735664 157.970364768418 136.757470252041 -0.434913653199297 0.157209464946713 -2.76645972522529 0.00566685842046991 0.0233757909844384 +TR3788|c0_g1_i1 wt_GSNO wt_ph8 128.115824993653 24.010679388938 76.0632521912957 1.36551096405932 0.534260069919225 2.55589186043003 0.0105916029199559 0.0388358773731717 +TR1492|c0_g1_i2 wt_GSNO wt_ph8 1368.89238848897 813.514514376559 1091.20345143276 0.692062260203308 0.290167592747528 2.38504325603812 0.0170771132686324 0.0563544737864868 +TR1678|c0_g1_i1 wt_GSNO wt_ph8 0.695005959508731 7.10082184137838 3.89791390044355 -1.19229893380239 0.533516728634619 -2.23479203145837 0.0254310052417055 0.0762930157251164 +TR5075|c0_g1_i1 wt_GSNO wt_ph8 8.81552188359314 126.23137395943 67.5234479215117 -1.10768013972448 0.513345367512952 -2.15776786900981 0.0309458842036983 0.0851011815601704 +TR1479|c0_g1_i1 wt_GSNO wt_ph8 353.92669362375 305.546165789569 329.736429706659 0.210154850632672 0.101920088147959 2.06195711219939 0.0392118193266939 0.0995376952139152 +TR1859|c3_g1_i1 wt_GSNO wt_ph8 0 2.05957798928713 1.02978899464357 -1.01742987508067 0.500302018271162 -2.03363136250477 0.0419887772494581 1 +TR2844|c0_g1_i1 wt_GSNO wt_ph8 220.566338218013 194.214843050373 207.390590634193 0.185176880395552 0.100284765132021 1.84651058564851 0.0648181037840442 0.152785530348104 +TR2107|c1_g1_i1 wt_GSNO wt_ph8 7.08292121571621 1.78415791317121 4.43353956444371 0.951944042839851 0.540599552522162 1.76090423752399 0.0782546125949942 0.170760316089935 +TR4669|c0_g2_i1 wt_GSNO wt_ph8 165.630009730314 0 82.8150048651569 0.762969565911357 0.439826422982926 1.73470607049221 0.0827928805284532 0.170760316089935 +TR2672|c0_g1_i1 wt_GSNO wt_ph8 2.07518941673641 7.44710458698621 4.76114700186131 -0.686459125319668 0.52860452101472 -1.29862514986048 0.194072602638997 0.376729169828641 +TR4859|c0_g1_i1 wt_GSNO wt_ph8 3.10763825129944 1.1806627783491 2.14415051482427 0.593225714064679 0.537217960853533 1.10425517628294 0.269482460872864 0.494051178266917 +TR3091|c0_g1_i1 wt_GSNO wt_ph8 312.47018793986 293.531643106953 303.000915523406 0.0878939148373507 0.0878811164283744 1.00014563320878 0.317240035048796 0.536180698490786 +TR4163|c0_g1_i1 wt_GSNO wt_ph8 221.469120691076 207.118822998308 214.293971844692 0.0959413488001967 0.0974696330347526 0.984320406397642 0.324957999085325 0.536180698490786 +TR1894|c2_g1_i1 wt_GSNO wt_ph8 2.85762748931802 1.47338219762144 2.16550484346973 0.431530486406946 0.537372709941065 0.803037590900872 0.421953007665329 0.663069012045517 +TR3249|c0_g1_i1 wt_GSNO wt_ph8 2.06512931203634 4.15451161800812 3.10982046502223 -0.38612563978518 0.523142120053183 -0.738089373774619 0.460460140618999 0.675718500003336 +TR5212|c0_g1_i1 wt_GSNO wt_ph8 102.736339436612 86.4452993262187 94.5908193814151 0.226915890105892 0.314756340859895 0.720925556212693 0.470955318184143 0.675718500003336 +TR1122|c0_g1_i1 wt_GSNO wt_ph8 1.29006258579706 0.5946183773076 0.942340481552333 0.279366026492593 0.486443515520964 0.57430311552905 0.565762701275693 1 +TR2011|c5_g1_i1 wt_GSNO wt_ph8 7.597917075274 4.42090354598533 6.00941031062966 0.293830308686626 0.525066976727929 0.559605386950241 0.575748629670957 0.791654365797565 +TR1837|c2_g1_i1 wt_GSNO wt_ph8 2.16507864525674 1.46465683073113 1.81486773799393 0.232644077202222 0.530765383353658 0.438318105322267 0.661155703054792 1 +TR1982|c2_g1_i1 wt_GSNO wt_ph8 5.5352448786851 10.687042573374 8.11114372602957 -0.163617497783336 0.41190705551325 -0.397219459082736 0.691205633846634 0.874699343226649 +TR1449|c0_g1_i1 wt_GSNO wt_ph8 98.9943307118646 106.843279101242 102.918804906553 -0.100378154615576 0.259464578599584 -0.38686650469729 0.69885503944156 0.874699343226649 +TR2182|c3_g2_i6 wt_GSNO wt_ph8 1.29006258579706 1.76655578876639 1.52830918728173 -0.199699696686908 0.518464312092113 -0.385175395932417 0.700107470922461 1 +TR4277|c0_g1_i1 wt_GSNO wt_ph8 153.969096204861 149.159426886469 151.564261545665 0.0459499001744168 0.126145529370448 0.364261027748966 0.715663099003622 0.874699343226649 +TR3854|c0_g1_i1 wt_GSNO wt_ph8 2260.55060252051 1927.46472630351 2094.00766441201 0.149461409336011 0.515737174792397 0.289801504799756 0.771968096584582 0.909819542403257 +TR127|c1_g1_i1 wt_GSNO wt_ph8 1.20754470361908 1.49113571265046 1.34934020813477 -0.140499936513031 0.525109891787989 -0.267562921038549 0.789035775295455 1 +TR2090|c0_g1_i1 wt_GSNO wt_ph8 9.46045896251181 5.6546754787973 7.55756722065455 0.0558182109444541 0.287850208274631 0.193914089133468 0.846243151562143 0.956832805790417 +TR3807|c0_g1_i1 wt_GSNO wt_ph8 0.347502979754365 0.292870809896544 0.320186894825454 0.0816135421729034 0.465942705668376 0.175157892118586 0.860955569985101 1 +TR131|c0_g1_i1 wt_GSNO wt_ph8 1275.67603302799 1312.2934796972 1293.9847563626 -0.035805337908038 0.355352253126282 -0.100760126305753 0.919740880292126 0.956832805790417 +TR5055|c0_g2_i1 wt_GSNO wt_ph8 5.17791343714095 5.60171771495863 5.38981557604979 -0.0489219520111245 0.535247232645477 -0.091400663146498 0.927174234841818 0.956832805790417 +TR939|c0_g1_i1 wt_GSNO wt_ph8 92.2508462008296 94.0990807885678 93.1749634946987 -0.0260132924520656 0.31360944301959 -0.0829480522065804 0.933892845523313 0.956832805790417 +TR2487|c0_g1_i1 wt_GSNO wt_ph8 875.181494043204 882.631049341941 878.906271692572 -0.0117684251443531 0.217416529127567 -0.0541284749212796 0.956832805790417 0.956832805790417
--- /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 11:35:34 2017 -0400 @@ -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.count_matrix Fri Mar 31 11:35:34 2017 -0400 @@ -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.count_matrix Fri Mar 31 11:35:34 2017 -0400 @@ -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
--- a/test-data/count/trinotate/genes.lengths.txt Thu Mar 23 10:15:32 2017 -0400 +++ b/test-data/count/trinotate/genes.lengths.txt Fri Mar 31 11:35:34 2017 -0400 @@ -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
--- a/test-data/filtered/Trinity_filtered_exp.fasta Thu Mar 23 10:15:32 2017 -0400 +++ b/test-data/filtered/Trinity_filtered_exp.fasta Fri Mar 31 11:35:34 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered/Trinity_filtered_hi_iso.fasta Fri Mar 31 11:35:34 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
--- a/tool_dependencies.xml Thu Mar 23 10:15:32 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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>
--- a/trinity.xml Thu Mar 23 10:15:32 2017 -0400 +++ b/trinity.xml Fri Mar 31 11:35:34 2017 -0400 @@ -3,13 +3,9 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - <requirement type="package" version="1.1.2">bowtie</requirement> - <requirement type="set_environment">TRINITY_MEM_OPTIONS</requirement> - </expand> - <expand macro="stdio"/> - <command><![CDATA[ - Trinity + <expand macro="requirements" /> + <command detect_errors="aggressive"><![CDATA[ + Trinity --no_version_check ## Inputs. #if $inputs.paired_or_single == "paired": @@ -71,10 +67,9 @@ #end if ## CPU and butterfly options. - --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS:---max_memory 1G} --bfly_opts "-V 10 --stderr" + --CPU \${GALAXY_SLOTS:-4} --max_memory \${TRINITY_MAX_MEMORY:-1G} --bflyHeapSpaceMax \${TRINITY_MAX_MEMORY:-1G} --bfly_opts '-V 10 --stderr' ## > $trinity_log 2>&1 - ]]></command> <inputs> <conditional name="inputs">