soapfuse an algorithm for identifying fusion transcripts from paired-end rna-seq datasoapfuse算法识别融合成绩单从paired-end rna-seq数据.pdfVIP

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soapfuse an algorithm for identifying fusion transcripts from paired-end rna-seq datasoapfuse算法识别融合成绩单从paired-end rna-seq数据.pdf

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soapfuse an algorithm for identifying fusion transcripts from paired-end rna-seq datasoapfuse算法识别融合成绩单从paired-end rna-seq数据

Jia et al. Genome Biology 2013, 14:R12 /content/14/2/R12 METHOD Open Access SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data 1,2† 1,2† 1,2† 2† 1,2,3 2,4 2 Wenlong Jia , Kunlong Qiu , Minghui He , Pengfei Song , Quan Zhou , Feng Zhou , Yuan Yu , 2 5 1,2 6 6,7 6,7 Dandan Zhu , Michael L Nickerson , Shengqing Wan , Xiangke Liao , Xiaoqian Zhu , Shaoliang Peng , Yingrui Li1,2, Jun Wang1,2,8,9 and Guangwu Guo1,2* 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 /soapfuse.html. Background of species [9-16]. In addition, RNA-Seq has been proven Gene fusions, arising from the juxtaposition of two distinct to be a sensitive and efficient approach to gene fusion regions in chromosomes, play important roles in carcino- discovery in many types of cancers [17-20]. Compared genesis and can serve as valuable dia