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Quantitative visualization of alternative exon expression from RNA-seq data.

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.

Availability and implementation

Software code and documentation freely available here: http://miso.readthedocs.org/en/fastmiso/sashimi.html

SUBMITTER: Katz Y

PROVIDER: S-EPMC4542614 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature

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Quantitative visualization of alternative exon expression from RNA-seq data.

Katz Yarden Y Wang Eric T ET Silterra Jacob J Schwartz Schraga S Wong Bang B Thorvaldsdóttir Helga H Robinson James T JT Mesirov Jill P JP Airoldi Edoardo M EM Burge Christopher B CB

Bioinformatics (Oxford, England) 20150122 14

<h4>Motivation</h4>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.<h4>Results</h4>To help address this problem, we present Sashimi plots, a quantitative visualization of al ...[more]

PMID: 25617416

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