Clinker: visualizing fusion genes detected in RNA-seq data
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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 fusion genes and the RNA-seq data used in their discovery.
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Now published in GigaScience doi: 10.1093/gigascience/giy079
Breon M Schmidt 1Murdoch Children’s Research Institute, Royal Children’s Hospital, Flemington Road, Parkville, Vic, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNadia M Davidson 1Murdoch Children’s Research Institute, Royal Children’s Hospital, Flemington Road, Parkville, Vic, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAnthony DK Hawkins 1Murdoch Children’s Research Institute, Royal Children’s Hospital, Flemington Road, Parkville, Vic, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRay Bartolo 1Murdoch Children’s Research Institute, Royal Children’s Hospital, Flemington Road, Parkville, Vic, …
Now published in GigaScience doi: 10.1093/gigascience/giy079
Breon M Schmidt 1Murdoch Children’s Research Institute, Royal Children’s Hospital, Flemington Road, Parkville, Vic, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNadia M Davidson 1Murdoch Children’s Research Institute, Royal Children’s Hospital, Flemington Road, Parkville, Vic, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAnthony DK Hawkins 1Murdoch Children’s Research Institute, Royal Children’s Hospital, Flemington Road, Parkville, Vic, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRay Bartolo 1Murdoch Children’s Research Institute, Royal Children’s Hospital, Flemington Road, Parkville, Vic, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteIan J Majewski 2Walter and Eliza Hall Institute of Medical Research, Royal Parade, Vic 3050, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePaul G Ekert 1Murdoch Children’s Research Institute, Royal Children’s Hospital, Flemington Road, Parkville, Vic, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlicia Oshlack 1Murdoch Children’s Research Institute, Royal Children’s Hospital, Flemington Road, Parkville, Vic, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alicia Oshlack
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy079 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101243 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101244 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101245
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