Yarden Katz1, Eric T Wang2, Jacob Silterra3, Schraga Schwartz3, Bang Wong3, Helga Thorvaldsdóttir3, James T Robinson3, Jill P Mesirov3, Edoardo M Airoldi4, Christopher B Burge5. 1. Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, Department of Biology, MIT, Cambridge, MA. 2. Department of Biology, MIT, Cambridge, MA. 3. The Broad Institute of Harvard, MIT, Cambridge, MA, USA. 4. The Broad Institute of Harvard, MIT, Cambridge, MA, USA, Department of Statistics, Harvard University, Cambridge, MA, USA and. 5. Department of Biology, MIT, Cambridge, MA, Department of Biological Engineering, MIT, Cambridge, MA.
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
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
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