alexa FuMa: reporting overlap in RNA-seq detected fusion genes
Pathology

Pathology

Diagnostic Pathology: Open Access

Author(s): Hoogstrate Y, Bttcher R, Hiltemann S, van der Spek PJ, Jenster G

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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.

This article was published in Bioinformatics and referenced in Diagnostic Pathology: Open Access

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