Method
Global and unbiased detection of splice junctions from RNA-seq data
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* Corresponding author: Adam Ameur adam.ameur@genpat.uu.se
Department of Genetics and Pathology, Rudbeck laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
Genome Biology 2010, 11:R34 doi:10.1186/gb-2010-11-3-r34
Published: 17 March 2010Abstract
We have developed a new strategy for de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts. When tested on mouse RNA-seq data, >31,000 splice events were predicted, of which 88% bridged between two regions separated by ≤100 kb, and 74% connected two exons of the same RefSeq gene. Our method also reports genomic rearrangements such as insertions and deletions.