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Nature methods DOI:10.1038/nmeth.1613

Computational methods for transcriptome annotation and quantification using RNA-seq.

Publication TypeJournal Article
Year of Publication2011
AuthorsGarber, M, Grabherr, MG, Guttman, M, Trapnell, C
JournalNature methods
Volume8
Issue6
Pages469-77
Date Published2011/06/01
ISSN1548-7091
Abstract

High-throughput RNA sequencing (RNA-seq) promises a comprehensive picture of the transcriptome, allowing for the complete annotation and quantification of all genes and their isoforms across samples. Realizing this promise requires increasingly complex computational methods. These computational challenges fall into three main categories: (i) read mapping, (ii) transcriptome reconstruction and (iii) expression quantification. Here we explain the major conceptual and practical challenges, and the general classes of solutions for each category. Finally, we highlight the interdependence between these categories and discuss the benefits for different biological applications.

URLhttp://dx.doi.org/10.1038/nmeth.1613
DOI10.1038/nmeth.1613
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/21623353?dopt=Abstract