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

被引：133

作者：

Jia, Wenlong ^{[1
,2
]}

Qiu, Kunlong ^{[1
,2
]}

He, Minghui ^{[1
,2
]}

Song, Pengfei ^{[2
]}

Zhou, Quan ^{[1
,2
,3
]}

Zhou, Feng ^{[2
,4
]}

Yu, Yuan ^{[2
]}

Zhu, Dandan ^{[2
]}

Nickerson, Michael L. ^{[5
]}

Wan, Shengqing ^{[1
,2
]}

Liao, Xiangke ^{[6
]}

Zhu, Xiaoqian ^{[6
,7
]}

Peng, Shaoliang ^{[6
,7
]}

Li, Yingrui ^{[1
,2
]}

Wang, Jun ^{[1
,2
,8
,9
]}

Guo, Guangwu ^{[1
,2
]}

机构：

[1] BGI Tech Solut Co Ltd, Shenzhen 518083, Peoples R China

[2] BGI Shenzhen, Shenzhen 518083, Peoples R China

[3] Univ Elect Sci & Technol China, Sch Life Sci & Technol, Chengdu 610054, Peoples R China

[4] S China Univ Technol, Guangzhou Higher Educ Mega Ctr, Sch Biosci & Bioengn, Guangzhou 510006, Guangdong, Peoples R China

[5] NCI, Canc & Inflammat Program, NIH, Frederick, MD 21702 USA

[6] Natl Univ Def Technol, Sch Comp Sci, Changsha 410073, Hunan, Peoples R China

[7] Natl Univ Def Technol, State Key Lab High Performance Comp, Changsha 410073, Hunan, Peoples R China

[8] Univ Copenhagen, Novo Nordisk Fdn Ctr Basic Metab Res, DK-1165 Copenhagen, Denmark

[9] Univ Copenhagen, Dept Biol, DK-1165 Copenhagen, Denmark

来源：

GENOME BIOLOGY | 2013年 / 14卷 / 02期

基金：

国家高技术研究发展计划(863计划);

关键词：

GENE FUSIONS; BREAST-CANCER; IDENTIFICATION; ULTRAFAST; DISCOVERY; ALIGNMENT; TOOL;

D O I：

10.1186/gb-2013-14-2-r12

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：15

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