Introduction

A new generation of tools that identify fusion genes in RNA-seq data is limited in either sensitivity and or specificity. To allow further downstream analysis and to estimate performance, predicted fusion genes from different tools have to be compared. However, the transcriptomic context complicates genomic location-based matching. FusionMatcher (FuMa) is a program that reports identical fusion genes based on gene-name annotations. FuMa automatically compares and summarizes all combinations of two or more datasets in a single run, without additional programming necessary. FuMa uses one gene annotation, avoiding mismatches caused by tool-specific gene annotations. FuMa matches 10% more fusion genes compared with exact gene matching due to overlapping genes and accepts intermediate output files that allow a stepwise analysis of corresponding tools.The code is available at: https://github.com/ErasmusMC-Bioinformatics/fuma and available for Galaxy in the tool sheds and directly accessible at https://bioinf-galaxian.erasmusmc.nl/galaxy/y.hoogstrate@erasmusmc.nl or a.stubbs@erasmusmc.nlSupplementary data are available at Bioinformatics online.

Publications

  1. FuMa: reporting overlap in RNA-seq detected fusion genes.
    Cite this
    Hoogstrate Y, Böttcher R, Hiltemann S, van der Spek PJ, Jenster G, Stubbs AP, 2016-04-01 - Bioinformatics (Oxford, England)

Credits

  1. Youri Hoogstrate
    Developer

    Department of Urology and Department of Bioinformatics, Erasmus University Medical Center

  2. René Böttcher
    Developer

  3. Saskia Hiltemann
    Developer

    Department of Urology and Department of Bioinformatics, Erasmus University Medical Center

  4. Peter J van der Spek
    Developer

    Department of Bioinformatics, Erasmus University Medical Center

  5. Guido Jenster
    Developer

  6. Andrew P Stubbs
    Investigator

    Department of Bioinformatics, Erasmus University Medical Center

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Summary
AccessionBT000345
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByAndrew P Stubbs