Difference between revisions of "MATS"

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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 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.
 
<!--Versions-->
 
==Available versions==
 
* 2.1.0
 
 
<!--Modules-->
 
<!--Modules-->
{{#if: {{#var: mod}}|==Execution Environment and Modules==
+
==Required Modules==
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+
[[Modules|modules documentation]]
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
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===Serial===
 +
*{{#var:app}}
 +
==System Variables==
 +
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_MATS_BIN - executable directory
 
* HPC_MATS_BIN - executable directory
 
<!--Run-->
 
<!--Run-->
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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
<!--Policy-->
 
<!--Policy-->
{{#if: {{#var: policy}}|==Usage policy==
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{{#if: {{#var: policy}}|==Usage Policy==
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)
 
|}}
 
|}}
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See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 
__NOTOC____NOEDITSECTION__
 
__NOTOC____NOEDITSECTION__
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=Validation=
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* Validated 4/5/2018

Latest revision as of 21:21, 6 December 2019

Description

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.

Required Modules

modules documentation

Serial

  • mats

System Variables

  • HPC_MATS_DIR - installation directory
  • HPC_MATS_BIN - executable directory





Validation

  • Validated 4/5/2018