Clinker: visualising fusion genes detected in RNA-seq data
- Author(s)
- Schmidt, BM; Davidson, NM; Hawkins, ADK; Bartolo, R; Majewski, IJ; Ekert, PG; Oshlack, A;
- Journal Title
- Gigascience
- Publication Type
- Journal Article in press
- Abstract
- Background: Genomic profiling efforts have revealed a rich diversity of oncogenic fusion genes. While there are many methods for identifying fusion genes from RNA-seq data, visualising these transcripts and their supporting reads remains challenging. Findings: 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). Conclusions: Clinker is freely available from Github https://github.com/Oshlack/Clinker under a MIT License.
- Publisher
- Oxford Academic
- Research Division(s)
- Cancer And Haematology
- PubMed ID
- 29982439
- Publisher's Version
- https://doi.org/10.1093/gigascience/giy079
- Open Access at Publisher's Site
https://doi.org/10.1093/gigascience/giy079- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
Creation Date: 2018-07-23 09:32:18
Last Modified: 2018-07-23 09:44:08