title: FuMa: reporting overlap in RNA-seq detected fusion genes.
abstract: 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.nl
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Urology and Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, 3000 CA, The Netherlands.
authors.forename: Youri
authors.initials: Y
authors.lastname: Hoogstrate
authors.affiliation: Department of Urology and.
authors.forename: René
authors.initials: R
authors.lastname: Böttcher
authors.affiliation: Department of Urology and Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, 3000 CA, The Netherlands.
authors.forename: Saskia
authors.initials: S
authors.lastname: Hiltemann
authors.affiliation: Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, 3000 CA, The Netherlands.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: van der Spek
authors.affiliation: Department of Urology and.
authors.forename: Guido
authors.initials: G
authors.lastname: Jenster
authors.affiliation: Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, 3000 CA, The Netherlands.
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Stubbs
mesh_terms: D016678:Genome; D023281:Genomics; D006801:Humans; D012313:RNA; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D012313:RNA