Introduction

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.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.A C++ and Python implementation of the method demonstrated in this article is available at http://exon.ucsd.edu/ShortFuse.mckinsel@ucsd.eduSupplementary data are available at Bioinformatics online.

Publications

  1. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.
    Cite this
    Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V, 2011-04-01 - Bioinformatics (Oxford, England)

Credits

  1. Marcus Kinsella
    Developer

    Bioinformatics and Systems Biology Program, Moores UCSD Cancer Center

  2. Olivier Harismendy
    Developer

  3. Masakazu Nakano
    Developer

  4. Kelly A Frazer
    Developer

  5. Vineet Bafna
    Investigator

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Summary
AccessionBT003076
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByVineet Bafna