Difference between revisions of "MATS"

Jump to navigation Jump to search
m (Text replace - "<!--Location--> {{App_Location|app={{#var:app}}|{{#var:ver}}}}" to "")
m (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==")
Line 27: Line 27:
* 2.1.0
* 2.1.0
{{#if: {{#var: mod}}|==Running the application using modules==
{{#if: {{#var: mod}}|==Execution Environment and Modules==
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->

Revision as of 02:03, 10 August 2012


mats website  

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.

Available versions

  • 2.1.0

Execution Environment and Modules

To use mats with the environment modules system at HPC the following commands are available:

Get module information for mats:

$module spider mats

Load the default application module:

$module load mats

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

  • HPC_MATS_DIR - directory where mats is located.
  • HPC_MATS_BIN - executable directory