1. SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data.
- Author
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Jia W, Qiu K, He M, Song P, Zhou Q, Zhou F, Yu Y, Zhu D, Nickerson ML, Wan S, Liao X, Zhu X, Peng S, Li Y, Wang J, and Guo G
- Subjects
- Cell Line, Tumor, Humans, Sensitivity and Specificity, Algorithms, Gene Fusion, RNA, Messenger genetics, Sequence Alignment methods, Sequence Analysis, RNA methods
- 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.
- Published
- 2013
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