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Genome Biol. 2010;11(10):R104. doi: 10.1186/gb-2010-11-10-r104. Epub 2010 Oct 21.

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data.

Author information

  • 1Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, New Haven, CT 06511, USA. andrea.sboner@yale.edu

Abstract

We have developed FusionSeq to identify fusion transcripts from paired-end RNA-sequencing. FusionSeq includes filters to remove spurious candidate fusions with artifacts, such as misalignment or random pairing of transcript fragments, and it ranks candidates according to several statistics. It also has a module to identify exact sequences at breakpoint junctions. FusionSeq detected known and novel fusions in a specially sequenced calibration data set, including eight cancers with and without known rearrangements.

PMID:
20964841
[PubMed - indexed for MEDLINE]
PMCID:
PMC3218660
Free PMC Article

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