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.
Ameur
Adam
A
Department of Genetics and Pathology, Rudbeck laboratory, Uppsala University, Uppsala, Sweden. adam.ameur@genpat.uu.se
Wetterbom
Anna
A
Feuk
Lars
L
Gyllensten
Ulf
U
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