Global and unbiased detection of splice junctions from RNA-seq data.
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.
Department of Genetics and Pathology, Rudbeck laboratory, Uppsala University, Uppsala, Sweden. adam.ameur@genpat.uu.se
Adam
A
Ameur
Anna
A
Wetterbom
Lars
L
Feuk
Ulf
U
Gyllensten
D000818:Animals; D001483:Base Sequence / Q000235:genetics*; D015321:Gene Rearrangement / Q000235:genetics*; D051379:Mice; D022821:RNA Splice Sites / Q000235:genetics*; D012326:RNA Splicing / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
D022821:RNA Splice Sites