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- Title
Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.
- Authors
McPherson, Andrew; Wu, Chunxiao; Hajirasouliha, Iman; Hormozdiari, Fereydoun; Hach, Faraz; Lapuk, Anna; Volik, Stanislav; Shah, Sohrab; Collins, Colin; Sahinalp, S Cenk
- Abstract
Comrad is a novel algorithmic framework for the integrated analysis of RNA-Seq and whole genome shotgun sequencing (WGSS) data for the purposes of discovering genomic rearrangements and aberrant transcripts. The Comrad framework leverages the advantages of both RNA-Seq and WGSS data, providing accurate classification of rearrangements as expressed or not expressed and accurate classification of the genomic or non-genomic origin of aberrant transcripts. A major benefit of Comrad is its ability to accurately identify aberrant transcripts and associated rearrangements using low coverage genome data. As a result, a Comrad analysis can be performed at a cost comparable to that of two RNA-Seq experiments, significantly lower than an analysis requiring high coverage genome data.
- Publication
Bioinformatics (Oxford, England), 2011, Vol 27, Issue 11, p1481
- ISSN
1367-4811
- Publication type
Journal Article
- DOI
10.1093/bioinformatics/btr184