Difference between revisions of "SpliceTrap"

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==Required Modules==
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==Environment Modules==
[[Modules|modules documentation]]
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
 
*{{#var:app}}
 
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
 
 
==System Variables==
 
==System Variables==
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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=Validation=
 
* Validated 4/5/2018
 

Revision as of 17:57, 10 June 2022

Description

splicetrap website  

SpliceTrap is a statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications for the study of alternative splicing. SpliceTrap approaches to exon inclusion level estimation as a Bayesian inference problem. For every exon it quantifies the extent to which it is included, skipped or subjected to size variations due to alternative 3’/5’ splice sites or Intron Retention. In addition, SpliceTrap can quantify alternative splicing within a single cellular condition, with no need of a background set of reads.

Environment Modules

Run module spider splicetrap to find out what environment modules are available for this application.

System Variables

  • HPC_SPLICETRAP_DIR - installation directory

How To Run

The main executable is SpliceTrap

The following databases are available by default:

  • hg18
  • hg19
  • mm9
  • rn4