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bioRxiv · 10.1101/002576

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

Yarden Katz·Eric T Wang·Jacob Stilterra·Schraga Schwartz·Bang Wong·Helga Thorvaldsdóttir·James T Robinson·Jill P Mesirov·Edoardo M Airoldi·Christopher B Burge
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Abstract

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 ...

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Yarden Katz, Eric T Wang, Jacob Stilterra, Schraga Schwartz, Bang Wong, Helga Thorvaldsdóttir, James T Robinson, Jill P Mesirov, Edoardo M Airoldi, Christopher B Burge. 2014-02-11. Sashimi plots: Quantitative visualization of alternative isoform expression from RNA-seq data. https://doi.org/10.1101/002576

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