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Computational methods for transcriptome annotation and quantification using RNA-seq

Nature Methods volume 8, pages 469477 (2011) | Download Citation

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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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Change history

  • 15 June 2011

    In the html version of this article initially published, the corresponding author was listed as Manfred G. Grabherr instead of Manuel Garber. The error has been corrected in the HTML version of the article.

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Acknowledgements

We thank L. Gaffney for help with figures; B. Haas for making available scripts to run transAbyss and for many discussions; Y. Katz, C. Nusbaum, A. Pauli and M. Zody for helpful discussions and comments on the manuscript; and J. Alfoldi, C. Burge, M. Cabili, K. Lindblad-Toh, J. Rinn, L. Pachter, S. Salzberg and O. Zuk for helpful comments on the manuscript.

Author information

Affiliations

  1. Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA.

    • Manuel Garber
    • , Manfred G Grabherr
    • , Mitchell Guttman
    •  & Cole Trapnell
  2. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

    • Mitchell Guttman
  3. Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.

    • Cole Trapnell

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Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Manuel Garber.

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DOI

https://doi.org/10.1038/nmeth.1613

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