title: 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.
authors: Wenlong
authors: W
authors: Jia
authors: Kunlong
authors: K
authors: Qiu
authors: Minghui
authors: M
authors: He
authors: Pengfei
authors: P
authors: Song
authors: Quan
authors: Q
authors: Zhou
authors: Feng
authors: F
authors: Zhou
authors: Yuan
authors: Y
authors: Yu
authors: Dandan
authors: D
authors: Zhu
authors: Michael L
authors: ML
authors: Nickerson
authors: Shengqing
authors: S
authors: Wan
authors: Xiangke
authors: X
authors: Liao
authors: Xiaoqian
authors: X
authors: Zhu
authors: Shaoliang
authors: S
authors: Peng
authors: Yingrui
authors: Y
authors: Li
authors: Jun
authors: J
authors: Wang
authors: Guangwu
authors: G
authors: Guo
mesh_terms: D000465:Algorithms; D045744:Cell Line, Tumor; D050939:Gene Fusion; D006801:Humans; D012333:RNA, Messenger / Q000235:genetics*; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012333:RNA, Messenger