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Old 12-04-2012, 03:00 AM   #1
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Default RNA-Seq: Improved transcriptome quantification and reconstruction from RNA-Seq reads

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Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations.

In Silico Biol. 2012 Jan 1;11(5):251-61

Authors: Mangul S, Caciula A, Glebova O, Mandoiu I, Zelikovsky A

Abstract
The paper addresses the problem of how to use RNA-Seq data for transcriptome reconstruction and quantification, as well as novel transcript discovery in partially annotated genomes. We present a novel annotation-guided general framework for transcriptome discovery, reconstruction and quantification in partially annotated genomes and compare it with existing annotation-guided and genome-guided transcriptome assembly methods. Our method, referred as Discovery and Reconstruction of Unannotated Transcripts (DRUT), can be used to enhance existing transcriptome assemblers, such as Cufflinks [3], as well as to accurately estimate the transcript frequencies. Empirical analysis on synthetic datasets confirms that Cufflinks enhanced by DRUT has superior quality of reconstruction and frequency estimation of transcripts.


PMID: 23202426 [PubMed - in process]



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