Quantitative visualization of alternative exon expression from RNA-seq data

Katz, Y., Wang, E. T., Silterra, J., Schwartz, S., Wong, B., Thorvaldsdottir, H., Robinson, J. T., Mesirov, J. P., Airoldi, E. M., Burge, C. B..

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:

Contact:, or

Supplementary information: Supplementary data are available at Bioinformatics online.