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

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 free

SUBMITTER: Katz Y 

PROVIDER: S-EPMC4542614 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature