Metadata-Version: 2.0
Name: rmats2sashimiplot
Version: 2.0.2
Summary: rmats2sashimiplot
Home-page: https://github.com/Xinglab/rmats2sashimiplot
Author: Yu-Ting Tseng, Emad Bahrami-Samani, Zhijie Xie, Yukai Jiang
Author-email: shiehshiehzhijie@gmail.com
License: GNU GPL
Download-URL: https://github.com/Xinglab/rmats2sashimiplot
Platform: UNKNOWN

====================
rmats2sashimiplot
====================

Requirements
-----------------

Install Python 2.6.x or Python 2.7.x

Install Samtools.

**setup.py** will automatically install matplotlib which is required to run this program.

rmats2sashimiplot is intended to be used in a Unix-based environment. It has

been tested on Mac OS and Linux.

**BAM file must be sorted before visualization/indexing.**

Installation
------------------

Install
########


The package, rmats2sashimiplot is installed by typing:

::

    python setup.py install

Update
########

To update rmats2sashimiplot, please download (or git pull) latest version from Github and type in:

::

    pip uninstall rmats2sashimiplot

::

    python setup.py install


Usage
-----
The following is a detailed description of the options used with rmats2sashimiplot.

Required Parameters
###########################
see README on homepage: https://github.com/Xinglab/rmats2sashimiplot

Running with sam files:
::

    $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

Running with bam files:
::

    $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

Using grouping function:
::

    $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

Grouping
###########################

By 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.

It's extremely helpful when you need to do comparisons between different groups of samples.

Examples
###########################


Example of using sam files, drawing sashimiplot by rMATS format event files
::

    $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


.. image:: plotwithevent.png
        :target: https://github.com/Xinglab/rmats2sashimiplot/blob/master/img/plotwithevent.png


Example of using bam files, drawing sashimiplot by user provided coordinates and gff3 format annotation file
::

    $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

.. image:: plotwithcoor.png
        :target: https://github.com/Xinglab/rmats2sashimiplot/blob/master/img/plotwithcoor.png

Example of using grouping function:
::

    $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

.. image:: plotwitheventgf.png
        :target: https://github.com/Xinglab/rmats2sashimiplot/blob/master/img/plotwitheventgf.png


content of grouping.gf:

::

    group1name: 1-2
    group2name: 3-6

That 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.

Group-info
<<<<<<<<<<<<

This section describes the format of `*.gf` file.

Each line stand for a group, which consists of group name and index of bam files.

**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.)

Index should be seperated by `','`. And use `'-'` to specify a sequence.

**Eg:**
::

    group1: 1,2
    group2: 3
    group3: 4-5
    group4: 4-5,6

    or

    group1:1,2
    group2:3
    group3:4-5
    group4:4-5,6

*(White space allowed.)*

Test Data
##########

Please download and untar the test data from: 

http://www.mimg.ucla.edu/faculty/xing/rmats2sashimiplot/testData.tar

Output
##########
All output sashimiplot pdf files are in Sashimi_plot folder

FAQ
##########
- Q: What does the y-axis represent?

- 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.

     .. image:: PRKM.png
             :target: https://github.com/Xinglab/rmats2sashimiplot/blob/master/img/RPKM.png

---------

- Q: How does rmats2sashimiplot calculate junction count, read density(modified RPKM) and inclusion level in the grouping mode?

- 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.


Contacts and bug reports
----------------------------------

Yi Xing

yxing@ucla.edu

Zhijie Xie

shiehshiehzhijie@gmail.com

If you found a bug or mistake in this project, we would like to know about it.

Before you send us the bug report though, please check the following:

1. Are you using the latest version? The bug you found may already have been
   fixed.
2. Check that your input is in the correct format and you have selected the
   correct options.
3. Please reduce your input to the smallest possible size that still produces
   the bug; we will need your input data to reproduce the problem, and the
   smaller you can make it, the easier it will be.


Copyright and License Information
--------------------------------------------
Copyright (C) 2015 University of California, Los Angeles (UCLA)

Zhijie Xie, Yu-Ting Tseng, Yi Xing

Zhijie Xie, Yu-Ting Tseng, Yi Xing

This program is free software: you can redistribute it and/or modify it under

the terms of the GNU General Public License as published by the Free Software

Foundation, either version 3 of the License, or (at your option) any later

version.

This program is distributed in the hope that it will be useful, but WITHOUT

ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS

FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with

this program. If not, see http://www.gnu.org/licenses/.



