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

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...

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Detalles Bibliográficos
Autores principales: Sboner, Andrea, Habegger, Lukas, Pflueger, Dorothee, Terry, Stephane, Chen, David Z, Rozowsky, Joel S, Tewari, Ashutosh K, Kitabayashi, Naoki, Moss, Benjamin J, Chee, Mark S, Demichelis, Francesca, Rubin, Mark A, Gerstein, Mark B
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218660/
https://www.ncbi.nlm.nih.gov/pubmed/20964841
http://dx.doi.org/10.1186/gb-2010-11-10-r104
Descripción
Sumario: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.

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