Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs | Zendy

Marcus Kinsella | Zendy; Olivier Harismendy | Zendy; Masakazu Nakano | Zendy; Kelly A. Frazer | Zendy; Vineet Bafna | Zendy

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Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs

Author(s) -

Marcus Kinsella,

Olivier Harismendy,

Masakazu Nakano,

Kelly A. Frazer,

Vineet Bafna

Publication year - 2011

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btr085

Subject(s) - python (programming language) , computer science , transcriptome , computational biology , spurious relationship , rna seq , fusion gene , biology , gene , genetics , gene expression , machine learning , operating system

Paired-end whole transcriptome sequencing provides evidence for fusion transcripts. However, due to the repetitiveness of the transcriptome, many reads have multiple high-quality mappings. Previous methods to find gene fusions either ignored these reads or required additional longer single reads. This can obscure up to 30% of fusions and unnecessarily discards much of the data.

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