Identification of novel transcripts in annotated genomes using RNA-Seq

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...

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Bibliographic Details
Published in:Bioinformatics (Oxford, England) England), 2011-09, Vol.27 (17), p.2325-2329
Main Authors: ROBERTS, Adam, PIMENTEL, Harold, TRAPNELL, Cole, PACHTER, Lior
Format: Article
Language:English
Subjects:
Algorithms
Animals
Biological and medical sciences
Fundamental and applied biological sciences. Psychology
Gene Expression Profiling
General aspects
Genome
Humans
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Molecular Sequence Annotation
RNA, Messenger - chemistry
RNA, Messenger - metabolism
Sequence Analysis, RNA
Software
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Summary: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. 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. cole@broadinstitute.org; lpachter@math.berkeley.edu Supplementary data are available at Bioinformatics online.
ISSN:1367-4803
1367-4811
DOI:10.1093/bioinformatics/btr355