SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data.

ABSTRACT: We have developed a new method, SOAPfuse, to identify fusion transcripts from paired-end RNA-Seq data. SOAPfuse applies an improved partial exhaustion algorithm to construct a library of fusion junction sequences, which can be used to efficiently identify fusion events, and employs a series of filters to nominate high-confidence fusion transcripts. Compared with other released tools, SOAPfuse achieves higher detection efficiency and consumed less computing resources. We applied SOAPfuse to RNA-Seq data from two bladder cancer cell lines, and confirmed 15 fusion transcripts, including several novel events common to both cell lines. SOAPfuse is available at http://soap.genomics.org.cn/soapfuse.html.

SUBMITTER: Jia W 

PROVIDER: S-EPMC4054009 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature