title: Quantitative visualization of alternative exon expression from RNA-seq data.
abstract: BACKGROUND
  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.
  
  
  METHODS
  Software code and documentation freely available here: http://miso.readthedocs.org/en/fastmiso/sashimi.html
authors.affiliation: Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, Department of Biology, MIT, Cambridge, MA.
authors.forename: Yarden
authors.initials: Y
authors.lastname: Katz
authors.affiliation: Department of Biology, MIT, Cambridge, MA.
authors.forename: Eric T
authors.initials: ET
authors.lastname: Wang
authors.affiliation: The Broad Institute of Harvard, MIT, Cambridge, MA, USA.
authors.forename: Jacob
authors.initials: J
authors.lastname: Silterra
authors.affiliation: The Broad Institute of Harvard, MIT, Cambridge, MA, USA.
authors.forename: Schraga
authors.initials: S
authors.lastname: Schwartz
authors.affiliation: The Broad Institute of Harvard, MIT, Cambridge, MA, USA.
authors.forename: Bang
authors.initials: B
authors.lastname: Wong
authors.affiliation: The Broad Institute of Harvard, MIT, Cambridge, MA, USA.
authors.forename: Helga
authors.initials: H
authors.lastname: Thorvaldsdóttir
authors.affiliation: The Broad Institute of Harvard, MIT, Cambridge, MA, USA.
authors.forename: James T
authors.initials: JT
authors.lastname: Robinson
authors.affiliation: The Broad Institute of Harvard, MIT, Cambridge, MA, USA.
authors.forename: Jill P
authors.initials: JP
authors.lastname: Mesirov
authors.affiliation: The Broad Institute of Harvard, MIT, Cambridge, MA, USA, Department of Statistics, Harvard University, Cambridge, MA, USA and.
authors.forename: Edoardo M
authors.initials: EM
authors.lastname: Airoldi
authors.affiliation: Department of Biology, MIT, Cambridge, MA, Department of Biological Engineering, MIT, Cambridge, MA.
authors.forename: Christopher B
authors.initials: CB
authors.lastname: Burge
mesh_terms: D017398:Alternative Splicing; D003196:Computer Graphics; D005091:Exons; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D059368:RNA Isoforms / Q000737:chemistry / Q000378:metabolism; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D059368:RNA Isoforms