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bioRxiv · 10.1101/218586

Clinker: visualising fusion genes detected in RNA-seq data

Schmidt, B. M.·Davidson, N. M.·Hawkins, A. D.·Bartolo, R.·Majewski, I. J.·Ekert, P. G.·Oshlack, A.
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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 Lymphoblastic Leukaemia (B-ALL).\n\nAvailability and ImplementationClinker is freely available from Github https://github.com/Oshlack/Clinker under a MIT License.\n\nContactalicia.oshlack@mcri.edu.au

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Schmidt, B. M., Davidson, N. M., Hawkins, A. D., Bartolo, R., Majewski, I. J., Ekert, P. G., Oshlack, A.. 2017-11-13. Clinker: visualising fusion genes detected in RNA-seq data. https://doi.org/10.1101/218586

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