RMATS
Description
MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both paired and unpaired study design.
License
If you use rMATS software, please cite:
Shen S., Park JW., Lu ZX., Lin L., Henry MD., Wu YN., Zhou Q., Xing Y. rMATS: Robust and Flexible Detection of Differential Alternative Splicing from Replicate RNA-Seq Data. PNAS, 111(51):E5593-601. doi: 10.1073/pnas.1419161111
Park JW., Tokheim C., Shen S., Xing Y. Identifying differential alternative splicing events from RNA sequencing data using RNASeq-MATS. Methods in Molecular Biology: Deep Sequencing Data Analysis, 2013;1038:171-179 doi: 10.1007/978-1-62703-514-9_10
Shen S., Park JW., Huang J., Dittmar KA., Lu ZX., Zhou Q., Carstens RP., Xing Y. MATS: A Bayesian Framework for Flexible Detection of Differential Alternative Splicing from RNA-Seq Data. Nucleic Acids Research, 2012;40(8):e61 doi: 10.1093/nar/gkr1291
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of rmats and load default version of rmats as
module avail rmats/ # list available modules module load rmats # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail rmats
and choose explicit version you want to use.
RNASeq-MATS.py #without arguments prints its usage
Documentation
http://rnaseq-mats.sourceforge.net/user_guide.htm