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Genome Biol. 2013 Feb 14;14(2):R12. doi: 10.1186/gb-2013-14-2-r12.

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.

PMID:
23409703
PMCID:
PMC4054009
DOI:
10.1186/gb-2013-14-2-r12
[Indexed for MEDLINE]
Free PMC Article

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