Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Genomics: the state of the art in RNA-seq analysis

Nature Methods volume 10, pages 1165–1166 (2013)Cite this article

Subjects

RNA-seq is a recent and immensely popular technology for cataloging and comparing gene expression. Two papers from the international RGASP consortium report on large-scale competitions to identify the best algorithms for RNA-seq analysis, with surprising variability in the results.

As a general rule, all cells of an organism contain the exact same DNA, and it is the expression of different RNAs (or different amounts of RNAs) that determines the identity of a cell. Important questions such as “Why are cancer cells different from normal cells?” can be answered by investigating all of the RNAs of a cell (its transcriptome) using a technique called RNA-seq. In this issue of Nature Methods, two papers from the RNA-seq Genome Annotation Assessment Project (RGASP) consortium evaluate the state of the art in RNA-seq analysis1,2.

This is a preview of subscription content

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

Buy

All prices are NET prices.

Figure 1

Abigail Yu

References

  1. Steijger, T. et al. Nat. Methods 10, 1177–1184 (2013).

    CAS  Article  Google Scholar 

  2. Engström, P.G. et al. Nat. Methods 10, 1185–1191 (2013).

    Article  Google Scholar 

  3. Nakamura, K. et al. Nucleic Acids Res. 39, e90 (2011).

    CAS  Article  Google Scholar 

  4. Stanke, M. et al. Nucleic Acids Res. 34, W435–W439 (2006).

    CAS  Article  Google Scholar 

  5. Schweikert, G. et al. Genome Res. 19, 2133–2143 (2009).

    CAS  Article  Google Scholar 

  6. Bradnam, K.R. et al. GigaScience 2, 10 (2013).

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Ian Korf is at the UC Davis Genome Center, University of California, Davis, Davis, California, USA.,

    Ian Korf

Authors
  1. Ian Korf
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ian Korf.

Ethics declarations

Competing interests

The author declares no competing financial interests.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Korf, I. Genomics: the state of the art in RNA-seq analysis. Nat Methods 10, 1165–1166 (2013). https://doi.org/10.1038/nmeth.2735

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nmeth.2735

Further reading

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing