Davidson, N. M. | Search bioRxiv

bioRxiv2017

Clinker: visualising fusion genes detected in RNA-seq data

Genomic profiling efforts have revealed a rich diversity of oncogenic fusion genes, and many are emerging as important therapeutic targets. While there are many ways to identify 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. 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).\n\nAvailability and ImplementationClinker is freely available from Github https://github.com/Oshlack/Clinker under a MIT License.\n\nContactalicia.oshlack@mcri.edu.au

bioinformatics↗

bioRxiv2017

Necklace: combining reference and assembled transcriptomes for RNA-Seq analysis

BackgroundRNA-Seq analyses can benefit from performing a genome-guided and de novo assembly, in particular for species where the reference genome or the annotation is incomplete. However, tools for integrating assembled transcriptome with reference annotation are lacking.\n\nFindingsNecklace is a software pipeline that runs genome-guided and de novo assembly and combines the resulting transcriptomes with reference genome annotations. Necklace constructs a compact but comprehensive superTranscriptome out of the assembled and reference data. Reads are subsequently aligned and counted in preparation for differential expression testing.\n\nConclusionsNecklace allows a comprehensive transcriptome to be built from a combination of assembled and annotated transcripts which results in a more comprehensive transcriptome for the majority of organisms. In addition RNA-seq data is mapped back to this newly created superTranscript reference to enable differential expression testing with standard methods. Necklace is available from https://github.com/Oshlack/necklace/wiki under GPL 3.0.

bioinformatics↗