FuMa – reporting overlap in RNA-seq detected fusion genes

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 to exact gene matching (EGM) due to overlapping genes and accepts intermediate output files that allow a step wise analysis of corresponding tools.

rna-seqDifferences between the matching approaches in the Berger (left) and Edgren (right) dataset. Each bar represents the number of fusion genes found in 2 or more samples. For this analysis a RefSeq gene annotation was used.

Availability – 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/

Contacty.hoogstrate@erasmusmc.nl; a.stubbs@erasmusmc.nl

Hoogstrate Y, Böttcher R, Hiltemann S, van der Spek P, Jenster G, Stubbs AP. (2015) FuMa: reporting overlap in RNA-seq detected fusion genes. Bioinformatics [Epub ahead of print]. [abstract]

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