jSplice is a novel method to detect differential alternative splicing events from RNA-seq experiments. The method relies on junction reads (mapped reads that span an exon-exon junction) to uncover differentially expressed alternative splicing modules (ASMs). AMSs were introduced by Hu et al. (Nucleic Acids Research 2012) and have the advantage to provide a wide definition for alternative splicing events while avoiding the whole transcript reconstruction problem. jSplice analyzes all ASMs of a given genome and compute the largest fold-change difference (referred to as “relative fold-change”) between two overlapping elements (junctions or exons) of an ASM.
# jsplice 1.0.2
jSplice is a fast method to detect differential alternative splicing events from RNA-seq
experiments. (see publication and/or manual for details).
jSplice is freely available under the GPL license at http://www.mhs.biol.ethz.ch/research/krek/jsplice
Requirements
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- Python 2.7 with numpy/scipy modules
- coverageBed from BEDtools package
Installation
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Nothing required
Execution
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Run 'python jSplice.py -h' to access the help menu
What's new in version 1.0.2
---------------------------
- Bug fixes
- Added sanity checks on RPKM calculations
- 3-decimal values in HTML output
- Better handling of Ensembl and UCSC chromosome naming schemes
