SpliceTrap

Description

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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. Template:App Location

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