Sashimi plots: Quantitative visualization of RNA sequencing read alignments

TL;DR

Sashimi plots provide a new method for visualizing RNA sequencing read alignments across multiple samples, aiding in the analysis of alternative splicing and isoform expression with customizable and publication-quality figures.

Contribution

This paper introduces Sashimi plots, a novel visualization tool for RNA-seq data that integrates alignments, gene annotations, and isoform estimates for comprehensive analysis.

Findings

Enables quick screening of differential splicing

Supports customizable publication-quality figures

Integrates with existing RNA-seq analysis tools

Abstract

We introduce Sashimi plots, a quantitative multi-sample visualization of mRNA sequencing reads aligned to gene annotations. Sashimi plots are made using alignments (stored in the SAM/BAM format) and gene model annotations (in GFF format), which can be custom-made by the user or obtained from databases such as Ensembl or UCSC. We describe two implementations of Sashimi plots: (1) a stand-alone command line implementation aimed at making customizable publication quality figures, and (2) an implementation built into the Integrated Genome Viewer (IGV) browser, which enables rapid and dynamic creation of Sashimi plots for any genomic region of interest, suitable for exploratory analysis of alternatively spliced regions of the transcriptome. Isoform expression estimates outputted by the MISO program can be optionally plotted along with Sashimi plots. Sashimi plots can be used to quickly screen differentially spliced exons along genomic regions of interest and can be used in publication quality figures. The Sashimi plot software and documentation is available from: http://genes.mit.edu/burgelab/miso/docs/sashimi.html