Quantitative visualization of alternative exon expression from RNA-seq data.
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| 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 Ó³»´«Ã½ Integrated Genome Viewer or with a stand-alone command line program. AVAILABILITY AND IMPLEMENTATION: Software code and documentation freely available here: |
| Year of Publication | 2015
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| Journal | Bioinformatics
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| Volume | 31
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| Issue | 14
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| Pages | 2400-2
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| Date Published | 2015 Jul 15
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| ISSN | 1367-4811
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| URL | |
| DOI | 10.1093/bioinformatics/btv034
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| PubMed ID | 25617416
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| PubMed Central ID | PMC4542614
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| Grant list | DP5 OD017865 / OD / NIH HHS / United States
R01 GM-085319 / GM / NIGMS NIH HHS / United States
R01 HG-002439 / HG / NHGRI NIH HHS / United States
R01 GM-096193 / GM / NIGMS NIH HHS / United States
U01 CA184897 / CA / NCI NIH HHS / United States
U01 CA-184897 / CA / NCI NIH HHS / United States
R01 CA-157304 / CA / NCI NIH HHS / United States
R01 CA157304 / CA / NCI NIH HHS / United States
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