Quantitative visualization of alternative exon expression from RNA-Seq data

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 (Pan et al. 2008; Wang et al. 2012). As RNA-Seq datasets grow in size, it remains challenging to visualize isoform expression across multiple samples.

To help address this problem, researchers from the Broad Institute of Harvard and MIT have developed 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 (IGV) or with a stand-alone command line program.


Anatomy of a Sashimi plot.

Availability – Software code and documentation freely available here: http://miso.readthedocs.org/en/fastmiso/sashimi.html

Contactmesirov@broadinstitute.org, airoldi@fas.harvard.edu, cburge@mit.edu

Katz Y, Wang ET, Silterra J, Schwartz S, Wong B, Thorvaldsdóttir H, Robinson JT, Mesirov JP, Airoldi EM, Burge CB. (2015) Quantitative visualization of alternative exon expression from RNA-seq data. Bioinformatics [Epub ahead of print]. [abstract]

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