Introduction

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

Publications

  1. Quantitative visualization of alternative exon expression from RNA-seq data.
    Cite this
    Katz Y, Wang ET, Silterra J, Schwartz S, Wong B, Thorvaldsdóttir H, Robinson JT, Mesirov JP, Airoldi EM, Burge CB, 2015-07-01 - Bioinformatics (Oxford, England)

Credits

  1. Yarden Katz
    Developer

    Department of Brain and Cognitive Sciences, MIT

  2. Eric T Wang
    Developer

    Department of Biology, MIT

  3. Jacob Silterra
    Developer

    The Broad Institute of Harvard, MIT, United States of America

  4. Schraga Schwartz
    Developer

    The Broad Institute of Harvard, MIT, United States of America

  5. Bang Wong
    Developer

    The Broad Institute of Harvard, MIT, United States of America

  6. Helga Thorvaldsdóttir
    Developer

    The Broad Institute of Harvard, MIT, United States of America

  7. James T Robinson
    Developer

    The Broad Institute of Harvard, MIT, United States of America

  8. Jill P Mesirov
    Developer

    The Broad Institute of Harvard, MIT, United States of America

  9. Edoardo M Airoldi
    Developer

    The Broad Institute of Harvard, MIT, United States of America

  10. Christopher B Burge
    Investigator

    Department of Biology, MIT

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Summary
AccessionBT006726
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByChristopher B Burge