Clinker: visualizing fusion genes detected in RNA-seq data.

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-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 fusio

SUBMITTER: Schmidt BM 

PROVIDER: S-EPMC6065480 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature