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

Jia, Wenlong, Qiu, Kunlong, He, Minghui, Song, Pengfei, Zhou, Quan, Zhou, Feng, Yu, Yuan, Zhu, Dandan, Nickerson, Michael L., Wan, Shengqing, Liao, Xiangke, Zhu, Xiaoqian, Peng, Shaoliang, Li, Yingrui, Wang, Jun and Guo, Guangwu (2013) SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data. Genome Biology, 14 . doi:10.1186/gb-2013-14-2-r12


Author Jia, Wenlong
Qiu, Kunlong
He, Minghui
Song, Pengfei
Zhou, Quan
Zhou, Feng
Yu, Yuan
Zhu, Dandan
Nickerson, Michael L.
Wan, Shengqing
Liao, Xiangke
Zhu, Xiaoqian
Peng, Shaoliang
Li, Yingrui
Wang, Jun
Guo, Guangwu
Title SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data
Journal name Genome Biology   Check publisher's open access policy
ISSN 1474-760X
1474-7596
Publication date 2013-02-14
Year available 2013
Sub-type Article (original research)
DOI 10.1186/gb-2013-14-2-r12
Open Access Status DOI
Volume 14
Total pages 15
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Chemistry and Molecular Biosciences
 
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