SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data
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- 作者：Wenlong Jia (1) (2)
Kunlong Qiu (1) (2)
Minghui He (1) (2)
Pengfei Song (2)
Quan Zhou (1) (2) (3)
Feng Zhou (2) (4)
Yuan Yu (2)
Dandan Zhu (2)
Michael L Nickerson (5)
Shengqing Wan (1) (2)
Xiangke Liao (6)
Xiaoqian Zhu (6) (7)
Shaoliang Peng (6) (7)
Yingrui Li (1) (2)
Jun Wang (1) (2) (8) (9)
Guangwu Guo (1) (2) - 刊名：Genome Biology
- 出版年：2013
- 出版时间：February 2013
- 年：2013
- 卷：14
- 期：2
- 全文大小：457 KB
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38. BLAT Search Genome [http://genome.ucsc.edu/cgi-bin/hgBlat?command=start] - 作者单位：Wenlong Jia (1) (2)
Kunlong Qiu (1) (2)
Minghui He (1) (2)
Pengfei Song (2)
Quan Zhou (1) (2) (3)
Feng Zhou (2) (4)
Yuan Yu (2)
Dandan Zhu (2)
Michael L Nickerson (5)
Shengqing Wan (1) (2)
Xiangke Liao (6)
Xiaoqian Zhu (6) (7)
Shaoliang Peng (6) (7)
Yingrui Li (1) (2)
Jun Wang (1) (2) (8) (9)
Guangwu Guo (1) (2)
1. BGI Tech Solutions Co., Ltd, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
2. BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
3. School of Life Science and Technology, University of Electronic Science and Technology of China, No.4, Section 2, North Jianshe Road, Chengdu, 610054, China
4. School of Bioscience and Bioengineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Panyu District, Guangzhou, 510006, China
5. Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD 21702, USA
6. School of Computer Science, National University of Defense Technology, No.47, Yanwachi street, Kaifu District, Changsha, Hunan, 410073, China
7. State Key Laboratory of High Performance Computing, National University of Defense Technology, No.47, Yanwachi street, Kaifu District, Changsha, Hunan, 410073, China
8. The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, DK-1165, Copenhagen, Denmark
9. Department of Biology, University of Copenhagen, DK-1165, Copenhagen, Denmark - ISSN：1465-6906
文摘
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.