title: Identification of novel transcripts in annotated genomes using RNA-Seq.
abstract: CONCLUSIONS
  We describe a new 'reference annotation based transcript assembly' problem for RNA-Seq data that involves assembling novel transcripts in the context of an existing annotation. This problem arises in the analysis of expression in model organisms, where it is desirable to leverage existing annotations for discovering novel transcripts. We present an algorithm for reference annotation-based transcript assembly and show how it can be used to rapidly investigate novel transcripts revealed by RNA-Seq in comparison with a reference annotation.
  
  
  BACKGROUND
  The methods described in this article are implemented in the Cufflinks suite of software for RNA-Seq, freely available from http://bio.math.berkeley.edu/cufflinks. The software is released under the BOOST license.
  
  
  BACKGROUND
  cole@broadinstitute.org; lpachter@math.berkeley.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Computer Science, UC Berkeley, Berkeley, CA, USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Roberts
authors.forename: Harold
authors.initials: H
authors.lastname: Pimentel
authors.forename: Cole
authors.initials: C
authors.lastname: Trapnell
authors.forename: Lior
authors.initials: L
authors.lastname: Pachter
mesh_terms: D000465:Algorithms; D000818:Animals; D020869:Gene Expression Profiling; D016678:Genome; D006801:Humans; D058977:Molecular Sequence Annotation; D012333:RNA, Messenger / Q000737:chemistry* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D012333:RNA, Messenger