Last update: May 17th, 2013




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.

Please see details in our publication below or online Documentations, we are updating SpliceTrap frequently, please check back regularly. Also, any comments or bug reports are welcome!


Wu J, Akerman M, Sun S, McCombie WR, Krainer AR, Zhang MQ (2011) SpliceTrap: a method to quantify alternative splicing under single cellular conditions: Bioinformatics 27, 3010-3016, doi:10.1093/bioinformatics/btr508 Link

Basic Requirements

1. Unix/Linux system with Perl and R installed, make sure they are in your PATH.
2. Qsub if you have a cluster (SUN Grid qsub is supported currently). Computing on a single computer is not recommended, although supported.
3. Either bowtie or RMAP installed, make sure they are in your PATH, then the script can directly use them by calling ‘bowtie/rmap'.
4. If you want to build your own TXdb database from BED/gtf format gene annotations, please make sure “bowtie-build” is in your PATH too and you would also need the fasta format genome sequences downloaded from UCSC genome browser.


The latest version can be downloaded from or using git (link)

We recommend you to download the latest code via git!

Or directly use it on CSH galaxy or UTD galaxy with simple clicks.

For version information, please check here

Supplementary data

There are 3 lanes of Paired end mRNA-seq data, read size is 36x2.

Lane 1: Read_1, Read_2
Lane 2: Read_1, Read_2
Lane 3: Read_1, Read_2

Other Information

Please refer to the README along with the code. Or you can check the online Documentations


wuj at cshl dot edu (expires soon, may not reachable!)

jiewu at mit dot edu


All rights reserved Zhang Lab, Krainer Lab, CSHL