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SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data
- Source :
- Genome Biology, Jia, W, Qiu, K, He, M, Song, P, Zhou, Q, Zhou, F, Yu, Y, Zhu, D, Nickerson, M L, Wan, S, Liao, X, Zhu, X, Peng, S, Li, Y, Wang, J & Guo, G 2013, ' SOAPfuse : an algorithm for identifying fusion transcripts from paired-end RNA-Seq data ', Genome Biology (Online Edition), vol. 14, no. 2, R12 . https://doi.org/10.1186/gb-2013-14-2-r12
- Publication Year :
- 2013
- Publisher :
- BioMed Central, 2013.
-
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.
Details
- Language :
- English
- ISSN :
- 14656914 and 14656906
- Volume :
- 14
- Issue :
- 2
- Database :
- OpenAIRE
- Journal :
- Genome Biology
- Accession number :
- edsair.doi.dedup.....63ff7f7bbcd712d0c3fb40f29837ec46