FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data.
Genome Biol, 2010;11(10):R104.
Sboner A[1], Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, Tewari AK, Kitabayashi N, Moss BJ, Chee MS, Demichelis F, Rubin MA, Gerstein MB
Affiliations
PMID: 20964841DOI: 10.1186/gb-2010-11-10-r104
Impact factor: 17.906
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.
MeSH terms
Base Sequence; Cell Line, Tumor; Computational Biology; Expressed Sequence Tags; Gene Expression Profiling; Gene Fusion; Gene Rearrangement; Humans; Male; Molecular Sequence Data; Neoplasms; Prostatic Neoplasms; RNA, Neoplasm; Reverse Transcriptase Polymerase Chain Reaction; Sequence Analysis, RNA
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