Supporting data for "Clinker: visualising fusion genes detected in RNA-seq data"

Dataset type: Transcriptomic, Software
Data released on June 27, 2018

Schmidt B; Davidson N; Hawkins A; Bartolo R; Majewski I; Ekert P; Oshlack A (2018): Supporting data for "Clinker: visualising fusion genes detected in RNA-seq data" GigaScience Database. http://dx.doi.org/10.5524/100460

DOI10.5524/100460

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. Clinker is a bioinformatics tool written in Python, R and Bpipe, that leverages the superTranscript method to visualise fusion genes (Davidson et al., 2017). 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).

Keywords:

Additional details

Read the peer-reviewed publication(s):

Schmidt, B. M., Davidson, N. M., Hawkins, A. D. K., Bartolo, R., Majewski, I. J., Ekert, P. G., & Oshlack, A. (2018). Clinker: visualizing fusion genes detected in RNA-seq data. GigaScience, 7(7). doi:10.1093/gigascience/giy079

Additional information:

https://github.com/Oshlack/Clinker

Accessions (data generated as part of this study):

BioProject: PRJNA451407
GEO : GSE113504





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN089699149606HumanhumanHomo sapiens Description:RNA-seq transcript sequences of EKL13-...
Alternative names:human
Alternative accession-BioSample:SAMN08969914
...
+
SAMN089699159606HumanhumanHomo sapiens Description:RNA-seq transcript sequences of MLM-22...
Alternative names:human
Alternative accession-BioSample:SAMN08969915
...
+
SAMN089699169606HumanhumanHomo sapiens Description:RNA-seq transcript sequences of EKL-7-...
Alternative names:human
Alternative accession-BioSample:SAMN08969916
...
+
SAMN089699179606HumanhumanHomo sapiens Description:RNA-seq transcript sequences of EKL-6-...
Alternative names:human
Alternative accession-BioSample:SAMN08969917
...
+
SAMN089699189606HumanhumanHomo sapiens Description:RNA-seq transcript sequences of EKL3-2...
Alternative names:human
Alternative accession-BioSample:SAMN08969918
...
+
SAMN089699199606HumanhumanHomo sapiens Description:RNA-seq transcript sequences of EKL15-...
Alternative names:human
Alternative accession-BioSample:SAMN08969919
...
+
Displaying 1-6 of 6 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
GitHub archivearchive42.17 MB2018-06-12
ReadmeTEXT1.24 KB2018-06-12
Displaying 1-2 of 2 File(s).
Funding body Awardee Award ID Comments
Australian National Health and Medical Research Council A Oshlack 1140626
Australian National Health and Medical Research Council I Majewski 1145912
Australian National Health and Medical Research Council A Oshlack 1126157 Career Development Fellowship
Independent Research Institutes Infrastructure Support Scheme 9000220
Cancer Council Victoria I Majewski 1124178
Date Action
June 27, 2018 Dataset publish
July 9, 2018 Manuscript Link added : 10.1093/gigascience/giy079