Introduction

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.

Publications

  1. FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data.
    Cite this
    Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, Tewari AK, Kitabayashi N, Moss BJ, Chee MS, Demichelis F, Rubin MA, Gerstein MB, 2010-01-01 - Genome biology

Credits

  1. Andrea Sboner
    Developer

    Program in Computational Biology and Bioinformatics, Yale University, United States of America

  2. Lukas Habegger
    Developer

  3. Dorothee Pflueger
    Developer

  4. Stephane Terry
    Developer

  5. David Z Chen
    Developer

  6. Joel S Rozowsky
    Developer

  7. Ashutosh K Tewari
    Developer

  8. Naoki Kitabayashi
    Developer

  9. Benjamin J Moss
    Developer

  10. Mark S Chee
    Developer

  11. Francesca Demichelis
    Developer

  12. Mark A Rubin
    Developer

  13. Mark B Gerstein
    Investigator

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Summary
AccessionBT005963
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC
User InterfaceTerminal Command Line
Download Count0
Submitted ByMark B Gerstein