Article
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.
BMC bioinformatics - 19 Apr 2012
Sacomoto Gustavo A T, Kielbassa Janice, Chikhi Rayan, Uricaru Raluca, Antoniou Pavlos, Sagot Marie-France, Peterlongo Pierre, Lacroix Vincent
Abstract excerpt
BACKGROUND: In this paper, we address the problem of identifying and quantifying polymorphisms in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on the fundamental idea that each polymorphism corresponds to a recognisable pattern in a De Bruijn graph constructed from the RNA-seq reads, we propose a general model for all polymorphisms in such graphs. We then...
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