1. SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data
- Author
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Xiangke Liao, Shengqing Wan, Shaoliang Peng, Quan Zhou, Pengfei Song, Feng Zhou, Michael L. Nickerson, Wenlong Jia, Yuan Yu, Guangwu Guo, Yingrui Li, Minghui He, Jun Wang, Kunlong Qiu, Xiaoqian Zhu, and Dandan Zhu
- Subjects
Fusion ,Sequence Analysis, RNA ,Bladder cancer cell ,Method ,RNA-Seq ,Sequence alignment ,Construct (python library) ,Biology ,Sensitivity and Specificity ,Fusion gene ,Cell Line, Tumor ,Humans ,natural sciences ,RNA, Messenger ,Gene Fusion ,Algorithm ,Sequence Alignment ,Algorithms - 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