Global and unbiased detection of splice junctions from RNA-seq data.

Ameur A, Wetterbom A, Feuk L, Gyllensten U

Genome Biol. 11 (3) R34 [2010-03-17; online 2010-03-17]

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 <or=100 kb, and 74% connected two exons of the same RefSeq gene. Our method also reports genomic rearrangements such as insertions and deletions.

NGI Uppsala (Uppsala Genome Center)

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PubMed 20236510

DOI 10.1186/gb-2010-11-3-r34

Crossref 10.1186/gb-2010-11-3-r34

gb-2010-11-3-r34

pmc PMC2864574

GEO GSE14605 [Mouse RNA-seq data]