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        "author": "Yu-Ting Tseng, Emad Bahrami-Samani, Zhijie Xie, Yukai Jiang",
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        "description": "====================\nrmats2sashimiplot\n====================\n\nRequirements\n-----------------\n\nInstall Python 2.6.x or Python 2.7.x\n\nInstall Samtools.\n\n**setup.py** will automatically install matplotlib which is required to run this program.\n\nrmats2sashimiplot is intended to be used in a Unix-based environment. It has\n\nbeen tested on Mac OS and Linux.\n\n**BAM file must be sorted before visualization/indexing.**\n\nInstallation\n------------------\n\nInstall\n########\n\n\nThe package, rmats2sashimiplot is installed by typing:\n\n::\n\n    python setup.py install\n\nUpdate\n########\n\nTo update rmats2sashimiplot, please download (or git pull) latest version from Github and type in:\n\n::\n\n    pip uninstall rmats2sashimiplot\n\n::\n\n    python setup.py install\n\n\nUsage\n-----\nThe following is a detailed description of the options used with rmats2sashimiplot.\n\nRequired Parameters\n###########################\nsee README on homepage: https://github.com/Xinglab/rmats2sashimiplot\n\nRunning with sam files:\n::\n\n    $rmats2sashimiplot --s1 s1_rep1.sam[,s1_rep2.sam]* --s2 s2.rep1.sam[,s2.rep2.sam]* -t eventType -e eventsFile --l1 SampleLabel1 --l2 SampleLabel2 --exon_s exonScale --intron_s intronScale -o outDir\n\nRunning with bam files:\n::\n\n    $rmats2sashimiplot --b1 s1_rep1.bam[,s1_rep2.bam]* --b2 s2.rep1.bam[,s2.rep2.bam]* -c coordinate:annotaionFile --l1 SampleLabel1 --l2 SampleLabel2 --exon_s exonScale --intron_s intronScale -o outDir\n\nUsing grouping function:\n::\n\n    $rmats2sashimiplot --b1 s1_rep1.bam[,s1_rep2.bam]* --b2 s2.rep1.bam[,s2.rep2.bam]* -c coordinate:annotaionFile --l1 SampleLabel1 --l2 SampleLabel2 --exon_s exonScale --intron_s intronScale -o outDir --group-info gf.gf\n\nGrouping\n###########################\n\nBy using this function, user can divide their samples into different groups. rmats2sashimiplot calculates the average inclusion level, the average read depth and the average number of junction-spanning reads of each group and display them in sashimi plot.\n\nIt's extremely helpful when you need to do comparisons between different groups of samples.\n\nExamples\n###########################\n\n\nExample of using sam files, drawing sashimiplot by rMATS format event files\n::\n\n    $rmats2sashimiplot --s1 ./testData/S1.R1.test.sam,./testData/S1.R2.test.sam,./testData/S1.R3.test.sam --s2 ./testData/S2.R1.test.sam,./testData/S2.R2.test.sam,./testData/S2.R3.test.sam -t SE -e ./testData/MATS_output/test_PC3E_GS689.SE.MATS.events.txt --l1 PC3E --l2 GS689 --exon_s 1 --intron_s 5 -o test_events_output\n\n\n.. image:: plotwithevent.png\n        :target: https://github.com/Xinglab/rmats2sashimiplot/blob/master/img/plotwithevent.png\n\n\nExample of using bam files, drawing sashimiplot by user provided coordinates and gff3 format annotation file\n::\n\n    $rmats2sashimiplot --b1 ./testData/S1.R1.test.bam,./testData/S1.R2.test.bam,./testData/S1.R3.test.bam --b2 ./testData/S2.R1.test.bam,./testData/S2.R2.test.bam,./testData/S2.R3.test.bam -c chr16:-:24944500:24955500:./testData/ensGene.gff3 --l1 PC3E --l2 GS689 --exon_s 1 --intron_s 5 -o test_coordinate_output\n\n.. image:: plotwithcoor.png\n        :target: https://github.com/Xinglab/rmats2sashimiplot/blob/master/img/plotwithcoor.png\n\nExample of using grouping function:\n::\n\n    $rmats2sashimiplot --b1 ./testData/S1.R1.test.bam,./testData/S1.R2.test.bam,./testData/S1.R3.test.bam --b2 ./testData/S2.R1.test.bam,./testData/S2.R2.test.bam,./testData/S2.R3.test.bam -t SE -e ./testData/MATS_output/test_PC3E_GS689.SE.MATS.events.txt --l1 PC3E --l2 GS689 --exon_s 1 --intron_s 5 -o test_events_output --group-info grouping.gf\n\n.. image:: plotwitheventgf.png\n        :target: https://github.com/Xinglab/rmats2sashimiplot/blob/master/img/plotwitheventgf.png\n\n\ncontent of grouping.gf:\n\n::\n\n    group1name: 1-2\n    group2name: 3-6\n\nThat means we group ./testData/S1.R1.test.bam and ./testData/S1.R2.test.bam together, and group ./testData/S1.R3.test.bam, ./testData/S2.R1.test.bam, ./testData/S2.R2.test.bam and ./testData/S2.R3.test.bam together.\n\nGroup-info\n<<<<<<<<<<<<\n\nThis section describes the format of `*.gf` file.\n\nEach line stand for a group, which consists of group name and index of bam files.\n\n**Important notes**: Index starts from 1. And the order of bam files corresponds to the order we specified in --b1/b2/s1/s2, i.e. concatenate --b1 and --b2 (or --s1 and --s2 if you're using them.). User can confirm this order by checking variable `bam_files` in `sashimi_plot_settings.txt` (under Sashimi_index_* folder.)\n\nIndex should be seperated by `','`. And use `'-'` to specify a sequence.\n\n**Eg:**\n::\n\n    group1: 1,2\n    group2: 3\n    group3: 4-5\n    group4: 4-5,6\n\n    or\n\n    group1:1,2\n    group2:3\n    group3:4-5\n    group4:4-5,6\n\n*(White space allowed.)*\n\nTest Data\n##########\n\nPlease download and untar the test data from: \n\nhttp://www.mimg.ucla.edu/faculty/xing/rmats2sashimiplot/testData.tar\n\nOutput\n##########\nAll output sashimiplot pdf files are in Sashimi_plot folder\n\nFAQ\n##########\n- Q: What does the y-axis represent?\n\n- A: MISO is the actual plotting backend of rmats2sashimiplot, so they have almost the same mechanism of plotting. The y-axis represents a modified RPKM value.\n\n     .. image:: PRKM.png\n             :target: https://github.com/Xinglab/rmats2sashimiplot/blob/master/img/RPKM.png\n\n---------\n\n- Q: How does rmats2sashimiplot calculate junction count, read density(modified RPKM) and inclusion level in the grouping mode?\n\n- A: rmats2sashimiplot uses a modified Sashimi plot proposed by SplicePlot(Wu, Nance, & Montgomery, 2014). Briefly, rmats2sashimiplot calculates the average read depth and the average number of junction-spanning reads for groups.\n\n\nContacts and bug reports\n----------------------------------\n\nYi Xing\n\nyxing@ucla.edu\n\nZhijie Xie\n\nshiehshiehzhijie@gmail.com\n\nIf you found a bug or mistake in this project, we would like to know about it.\n\nBefore you send us the bug report though, please check the following:\n\n1. Are you using the latest version? The bug you found may already have been\n   fixed.\n2. Check that your input is in the correct format and you have selected the\n   correct options.\n3. Please reduce your input to the smallest possible size that still produces\n   the bug; we will need your input data to reproduce the problem, and the\n   smaller you can make it, the easier it will be.\n\n\nCopyright and License Information\n--------------------------------------------\nCopyright (C) 2015 University of California, Los Angeles (UCLA)\n\nZhijie Xie, Yu-Ting Tseng, Yi Xing\n\nZhijie Xie, Yu-Ting Tseng, Yi Xing\n\nThis program is free software: you can redistribute it and/or modify it under\n\nthe terms of the GNU General Public License as published by the Free Software\n\nFoundation, either version 3 of the License, or (at your option) any later\n\nversion.\n\nThis program is distributed in the hope that it will be useful, but WITHOUT\n\nANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS\n\nFOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.\n\nYou should have received a copy of the GNU General Public License along with\n\nthis program. If not, see http://www.gnu.org/licenses/.\n\n\n\n",
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