Year: 2015
Type: article
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 Contact: [email protected], [email protected] or [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics
Authors: Yarden Katz, Eric T. Wang, Jacob Silterra, Schraga Schwartz, Bang Wong, Helga Thorvaldsdóttir, James T. Robinson, Jill P. Mesirov, Edoardo M. Airoldi, Christopher B. Burge
Language: English
Topic: RNA Research and Splicing
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: bronze
Awards: A next-generation Integrative Genomics Viewer for biomedical and cancer research., CAREER: Quantifying diffusion and dynamics on healthcare, innovation and communication networks, Quant. methods for systems-level analyses of regulation & signaling dynamics, Ppst-transcriptional regulation of gene expression in neuromuscular disease, Dynamics of Gene and Isoform Regulation during EMT and tumor progression, Regulation and Function of Alternative mRNA Isoform Expression in Mammals, Function of Sequence-specific RNA Binding Proteins
OpenAlex ID: W2155806289