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Bioinformatics. 2011 Apr 15;27(8):1068-75. doi: 10.1093/bioinformatics/btr085. Epub 2011 Feb 16.

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

Author information

  • 1Bioinformatics and Systems Biology Program, Moores UCSD Cancer Center, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA. mckinsel@ucsd.edu

Abstract

MOTIVATION:

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.

RESULTS:

We present a method for using paired-end reads to find fusion transcripts without requiring unique mappings or additional single read sequencing. Using simulated data and data from tumors and cell lines, we show that our method can find fusions with ambiguously mapping read pairs without generating numerous spurious fusions from the many mapping locations.

AVAILABILITY:

A C++ and Python implementation of the method demonstrated in this article is available at http://exon.ucsd.edu/ShortFuse.

CONTACT:

mckinsel@ucsd.edu

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
21330288
[PubMed - indexed for MEDLINE]
PMCID:
PMC3072550
Free PMC Article

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