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Identification of novel transcripts in annotated genomes using RNA-Seq

Roberts, Adam and Pimentel, Harold and Trapnell, Cole and Pachter, Lior (2011) Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics, 27 (17). pp. 2325-2329. ISSN 1367-4803. https://resolver.caltech.edu/CaltechAUTHORS:20170306-101954304

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Abstract

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. Availability: 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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1093/bioinformatics/btr355DOIArticle
https://academic.oup.com/bioinformatics/article/27/17/2325/223194/Identification-of-novel-transcripts-in-annotatedPublisherArticle
Additional Information:© The Author 2011. Published by Oxford University Press. AR was funded in part by an NSF graduate fellowship. Conflict of Interest: none declared.
Funders:
Funding AgencyGrant Number
NSF Graduate Research FellowshipUNSPECIFIED
Issue or Number:17
Record Number:CaltechAUTHORS:20170306-101954304
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170306-101954304
Official Citation:Adam Roberts, Harold Pimentel, Cole Trapnell, Lior Pachter; Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics 2011; 27 (17): 2325-2329. doi: 10.1093/bioinformatics/btr355
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74772
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:06 Mar 2017 18:32
Last Modified:03 Oct 2019 16:42

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