Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies

Chimeric transcripts, including partial and internal tandem duplications (PTDs, ITDs) and gene fusions, are important in the detection, prognosis, and treatment of human cancers. We describe Barnacle, a production-grade analysis tool that detects such chimeras in de novo assemblies of RNA-seq data,...

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Bibliographic Details
Published in:	BMC genomics Vol. 14; no. 1; p. 550
Main Authors:	Swanson, Lucas, Robertson, Gordon, Mungall, Karen L, Butterfield, Yaron S, Chiu, Readman, Corbett, Richard D, Docking, T Roderick, Hogge, Donna, Jackman, Shaun D, Moore, Richard A, Mungall, Andrew J, Nip, Ka Ming, Parker, Jeremy D K, Qian, Jenny Qing, Raymond, Anthony, Sung, Sandy, Tam, Angela, Thiessen, Nina, Varhol, Richard, Wang, Sherry, Yorukoglu, Deniz, Zhao, Yongjun, Hoodless, Pamela A, Sahinalp, S Cenk, Karsan, Aly, Birol, Inanc
Format:	Journal Article
Language:	English
Published:	England BioMed Central Ltd 14-08-2013 BioMed Central
Subjects:	Analysis Breast Neoplasms - genetics Cancer Chimeras (Organisms) Colleges & universities Exons - genetics Gene Duplication - genetics Gene Expression Profiling - methods Gene Fusion - genetics Genes Genetic transcription Genomes Genomics Humans Leukemia, Myeloid, Acute - genetics Medical research Medicine, Experimental Methodology Methods Molecular Sequence Annotation RNA sequencing RNA, Messenger - genetics Science Software Statistics as Topic Transfer RNA
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