SpliceTrap

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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.

Required Modules

modules documentation

Serial

  • splicetrap

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





Validation

  • Validated 4/5/2018