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Updated: Feb 8, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
Clinker: visualizing fusion genes detected in RNA-seq data
Breon M Schmidt1, Nadia M Davidson1,2, Anthony D K Hawkins1
1Murdoch Children's Research Institute, The Royal Children's Hospital, Flemington, Road, Parkville Vic 3052 Australia.
Background:
Genomic profiling efforts have revealed a rich diversity of oncogenic fusion genes. While there are many methods for identifying fusion genes from RNA-sequencing (RNA-seq) data, visualizing 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 visualize fusion genes. We demonstrate the use of Clinker to obtain interpretable visualizations 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 leukemia.
Conclusions:
Clinker is freely available software that allows visualization of fusion genes and the RNA-seq data used in their discovery.
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