Quantitative visualization of alternative exon expression from RNA-seq data.

Bioinformatics
Authors
Keywords
Abstract

MOTIVATION: Analysis of RNA sequencing (RNA-Seq) data revealed that the vast majority of human genes express multiple mRNA isoforms, produced by alternative pre-mRNA splicing and other mechanisms, and that most alternative isoforms vary in expression between human tissues. As RNA-Seq datasets grow in size, it remains challenging to visualize isoform expression across multiple samples.

RESULTS: To help address this problem, we present Sashimi plots, a quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. Sashimi plots can be made using the Broad Integrated Genome Viewer or with a stand-alone command line program.

AVAILABILITY AND IMPLEMENTATION: Software code and documentation freely available here: http://miso.readthedocs.org/en/fastmiso/sashimi.html

Year of Publication
2015
Journal
Bioinformatics
Volume
31
Issue
14
Pages
2400-2
Date Published
2015 Jul 15
ISSN
1367-4811
URL
DOI
10.1093/bioinformatics/btv034
PubMed ID
25617416
PubMed Central ID
PMC4542614
Links
Grant list
DP5 OD017865 / OD / NIH HHS / United States
R01 GM-085319 / GM / NIGMS NIH HHS / United States
R01 HG-002439 / HG / NHGRI NIH HHS / United States
R01 GM-096193 / GM / NIGMS NIH HHS / United States
U01 CA184897 / CA / NCI NIH HHS / United States
U01 CA-184897 / CA / NCI NIH HHS / United States
R01 CA-157304 / CA / NCI NIH HHS / United States
R01 CA157304 / CA / NCI NIH HHS / United States