Difference between revisions of "SpliceTrap"

From UFRC
Jump to navigation Jump to search
m (Text replace - "{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}" to "{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} ")
m (Text replace - "<!--Location--> {{App_Location|app={{#var:app}}|{{#var:ver}}}}" to "")
Line 22: Line 22:
  
 
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.
 
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.
<!--Location-->
+
 
{{App_Location|app={{#var:app}}|{{#var:ver}}}}
 
 
<!--Versions-->
 
<!--Versions-->
 
==Available versions==
 
==Available versions==

Revision as of 02:00, 10 August 2012

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.

Available versions

  • 0.90.5

Running the application using modules

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

Get module information for splicetrap:

$module spider splicetrap

Load the default application module:

$module load splicetrap

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

  • HPC_SPLICETRAP_DIR - directory where splicetrap is located.

How To Run

The main executable is SpliceTrap

The following databases are available by default:

  • hg18
  • hg19
  • mm9
  • rn4