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

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          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.

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          Author and article information

          Journal
          Nat Methods
          Nature methods
          Springer Science and Business Media LLC
          1548-7105
          1548-7091
          Jun 2011
          : 8
          : 6
          Affiliations
          [1 ] Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA. mgarber@broadinstitute.org
          Article
          nmeth.1613
          10.1038/nmeth.1613
          21623353
          702054f6-1b9c-4c1c-8351-8a51c37122c4
          History

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