Difference between revisions of "SpliceTrap"
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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. | 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. | ||
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Revision as of 02:36, 10 August 2012
Description
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.
Execution Environment and 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