Sashimi plots: Quantitative visualization of alternative isoform expression from RNA-seq data

To the Editor: To the Editor: Software documentation and... References 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., 2008). As RNA-Seq datasets grow in size, it remains challenging to visualize isoform expression across multiple samples. We present Sashimi plots, a quantitative multi-sample visualization of RNA-Seq reads aligned to gene annotations, which enables quantitative comparison of isoform usage across samples or experimental conditions. Given an input annotation and spliced alignments of reads from a sample, a region of interest is visualized in a Sashimi plot as follows: (i) alignments in ...