Sashimi Plot

https://software.broadinstitute.org/software/igv/Sashimi

Methods

linear single view single scale single focus contiguous no abstraction no arrangement within interconnection segment sparse type point sparse type

Tool

Access Format web application
Supported Files bed fasta sambamcram vcf other
License MIT
Tool name

Sashimi Plot
Tool Link https://software.broadinstitute.org/software/igv/Sashimi
Documentation https://software.broadinstitute.org/software/igv/Sashimi

Paper

Sashimi plots: Quantitative visualization of RNA sequencing read alignments

Katz Y, Wang ET, Silterra J, Schwartz S, Wong B, Mesirov JP, et al. Sashimi plots: Quantitative visualization of RNA sequencing read alignments [Internet]. arXiv [q-bio.GN]. 2013. Available: http://arxiv.org/abs/1306.3466

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.