Journal article

Clinker: visualising fusion genes detected in RNA-seq data

Breon Schmidt, Nadia Davidson, Anthony DK Hawkins, Ray Bartolo, Ian Majewski, Paul Ekert, Alicia Oshlack

Published : 2017

Abstract

ABSTRACT Genomic profiling efforts have revealed a rich diversity of oncogenic fusion genes, and many are emerging as important therapeutic targets. While there are many ways to identify fusion genes from RNA-seq data, visualising these transcripts and their supporting reads remains challenging. Clinker is a bioinformatics tool written in Python, R and Bpipe, that leverages the superTranscript method to visualise fusion genes. We demonstrate the use of Clinker to obtain interpretable visualisations of the RNA-seq data that lead to fusion calls. In addition, we use Clinker to explore multiple fusion transcripts with novel breakpoints within the P2RY8-CRLF2 fusion gene in B-cell Acute Lymphobl..

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