Brief Communication | Published:

Differential analysis of RNA-seq incorporating quantification uncertainty

Nature Methods volume 14, pages 687690 (2017) | Download Citation

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Abstract

We describe sleuth (http://pachterlab.github.io/sleuth), a method for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance. sleuth is implemented in an interactive shiny app that utilizes kallisto quantifications and bootstraps for fast and accurate analysis of data from RNA-seq experiments.

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Change history

  • 23 August 2017

    In the version of this article initially published, the final term in equation (2) in the Online Methods was incorrectly specified as xti. The correct term is ζti. Also, the two callouts to Supplementary Note 3 in the Online Methods section were incorrect and should have referred to Supplementary Note 2. These errors have been corrected in the HTML and PDF versions of the article.

Accessions

Primary accessions

European Nucleotide Archive

Gene Expression Omnibus

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Acknowledgements

H.P. and L.P. were partially supported by NIH grant nos. R01 DK094699 and R01 HG006129. We thank D. Li, A. Tseng, and P. Sturmfels for help with implementing some of the interactive features in sleuth.

Author information

Affiliations

  1. Department of Computer Science, University of California, Berkeley, Berkeley, California, USA.

    • Harold Pimentel
  2. Innovative Genomics Institute and Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, California, USA.

    • Nicolas L Bray
  3. Department of Statistics, University of California, Berkeley, Berkeley, California, USA.

    • Suzette Puente
  4. Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjavík, Iceland.

    • Páll Melsted
  5. Division of Biology and Biological Engineering, Caltech, Pasadena, California, USA.

    • Lior Pachter

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Contributions

H.P. led the development of the sleuth statistical model and was assisted by S.P., N.L.B., P.M., and L.P. The method comparison and testing framework was designed by H.P., N.L.B., P.M., and L.P. The interactive sleuth live software was designed and implemented by H.P., as was the sleuth R package. H.P. automated production of the results. H.P., N.L.B., P.M., and L.P. analyzed results and wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Lior Pachter.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–8 and Supplementary Notes 1–3

Zip files

  1. 1.

    Supplementary Software

    Sleuth software used in the article along with the analysis to reproduce figures.

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DOI

https://doi.org/10.1038/nmeth.4324

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