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

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...

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Bibliographic Details
Published in:In silico biology 2012, Vol.11 (5-6), p.251-261
Main Authors: Mangul, Serghei, Caciula, Adrian, Glebova, Olga, Mandoiu, Ion, Zelikovsky, Alex
Format: Article
Language:English
Subjects:
Gene Expression Profiling
High-Throughput Nucleotide Sequencing - methods
Humans
Sequence Analysis, RNA
Transcriptome - genetics
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Summary: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.
ISSN:1386-6338
1434-3207
DOI:10.3233/ISB-2012-0459