Quantitative visualization of alternative exon expression from RNA-seq data

• DOI: 10.1093/bioinformatics/btv034
• Publication Date: 2015-01-24T04:27:59Z
• Authors: Yarden Katz; Eric T. Wang; Jacob Silterra; Schraga Schwartz; Bang Wong; Helga Thorvaldsdó...; James T. Robinson; Jill P. Mesirov; Edoardo M. Airoldi; Christopher B. Burge
• Keywords: RNA-Seq

Abstract Motivation: Analysis of RNA sequencing (RNA-Seq) data revealed that the vast majority human genes express multiple mRNA isoforms, produced by alternative pre-mRNA splicing and other mechanisms, most isoforms vary in expression between tissues. As RNA-Seq datasets grow size, it remains challenging to visualize isoform across samples. Results: To help address this problem, we present Sashimi plots, a quantitative visualization aligned reads enables comparison exon usage samples or experimental conditions. plots can be made using Broad Integrated Genome Viewer with stand-alone command line program. Availability implementation: Software code documentation freely available here: http://miso.readthedocs.org/en/fastmiso/sashimi.html Contact: [e-mail], [e-mail] [e-mail] Supplementary information: are at Bioinformatics online.