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Identification of novel transcripts in annotated genomes using RNA-Seq.
Bioinformatics. 2011 Jun 21;
Authors: Roberts A, Pimentel H, Trapnell C, Pachter L
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. SUPPLEMENTARY INFORMATION: The assemblies compared in the Results section are provided along with the publication at the journal's website. AVAILABILITY: The methods described in this paper 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. CONTACT: [email protected], [email protected].
PMID: 21697122 [PubMed - as supplied by publisher]
More...
Identification of novel transcripts in annotated genomes using RNA-Seq.
Bioinformatics. 2011 Jun 21;
Authors: Roberts A, Pimentel H, Trapnell C, Pachter L
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. SUPPLEMENTARY INFORMATION: The assemblies compared in the Results section are provided along with the publication at the journal's website. AVAILABILITY: The methods described in this paper 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. CONTACT: [email protected], [email protected].
PMID: 21697122 [PubMed - as supplied by publisher]
More...