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.

Ballgown bridges the gap between transcriptome assembly and expression analysis

Nature Biotechnology volume 33, pages 243–246 (2015)Cite this article

Subjects

To the Editor:

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Experimental results obtained with the Ballgown framework.

References

  1. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Nat. Methods 5, 621–628 (2008).

    Article  CAS  Google Scholar 

  2. Trapnell, C. et al. Nat. Biotechnol. 28, 511–515 (2010).

    Article  CAS  Google Scholar 

  3. Grabherr, M.G. et al. Nat. Biotechnol. 29, 644–652 (2011).

    Article  CAS  Google Scholar 

  4. Gentleman, R.C. et al. Genome Biol. 5, R80 (2004).

    Article  Google Scholar 

  5. Dermitzakis, M., Getz, G., Ardlie, K., Guigo, R. & GTEx Consortium. Bits of DNA https://liorpachter.wordpress.com/author/edermitzakis/. (2013).

    Google Scholar 

  6. Pertea, M. et al. Nat. Biotechnol. 33, 290–295 (2015).

    Article  CAS  Google Scholar 

  7. Li, B. & Dewey, C.N. BMC Bioinformatics 12, 323 (2011).

    Article  CAS  Google Scholar 

  8. Smyth, G.K. in Bioinformatics and Computational Biology Solutions Using R and Bioconductor (eds. Gentleman, R., Carey, V., Huber, W., Irizarry, R. & Dudoit, S.) 397–420 (Springer, 2005).

    Book  Google Scholar 

  9. Law, C.W., Chen, Y., Shi, W. & Smyth, G.K. Genome Biol. 15, R29 (2014).

    Article  Google Scholar 

  10. Robinson, M.D., McCarthy, D.J. & Smyth, G.K. Bioinformatics 26, 139–140 (2010).

    Article  CAS  Google Scholar 

  11. Anders, S. & Huber, W. Genome Biol. 11, R106 (2010).

    Article  CAS  Google Scholar 

  12. Chen, Y., McCarthy, D., Robinson, M. & Smyth, G.K. edgeR: differential expression analysis of digital gene expression data User's Guide. http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf (2011).

    Google Scholar 

  13. Trapnell, C. et al. Nat. Protoc. 7, 562–578 (2012).

    Article  CAS  Google Scholar 

  14. Leng, N. et al. Bioinformatics 29, 1035–1043 (2013).

    Article  CAS  Google Scholar 

  15. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Genome Biol. 10, R25 (2009).

    Article  Google Scholar 

  16. Kim, D. et al. Genome Biol. 14, R36 (2013).

    Article  Google Scholar 

  17. Trapnell, C. et al. Nat. Biotechnol. 31, 46–53 (2013).

    Article  CAS  Google Scholar 

  18. Lister, R. et al. Science 341, 1237905 (2013).

    Article  Google Scholar 

  19. Young, R.S. et al. Genome Biol. Evol. 4, 427–442 (2012).

    Article  CAS  Google Scholar 

  20. Lister, R. et al. Nature 471, 68–73 (2011).

    Article  CAS  Google Scholar 

  21. Djebali, S. et al. Nature 489, 101–108 (2012).

    Article  CAS  Google Scholar 

  22. Graveley, B.R. et al. Nature 471, 473–479 (2011).

    Article  CAS  Google Scholar 

  23. C't Hoen, A.P., Friedländer, M.R. & Almlöf, J. Nature 31, 1015–1022 (2013).

    Google Scholar 

  24. Lappalainen, T. et al. Nature 501, 506–511 (2013).

    Article  CAS  Google Scholar 

  25. Storey, J.D. & Tibshirani, R. Proc. Natl. Acad. Sci. USA 100, 9440–9445 (2003).

    Article  CAS  Google Scholar 

  26. Frazee, A.C., Sabunciyan, S., Hansen, K.D., Irizarry, R.A. & Leek, J.T. Biostatistics 15, 413–426 (2014).

    Article  Google Scholar 

  27. Kim, S.C. et al. PLoS ONE 8, e55596 (2013).

    Article  CAS  Google Scholar 

  28. Yan, L. et al. Nat. Struct. Mol. Biol. 20, 1131–1139 (2013).

    Article  CAS  Google Scholar 

  29. Coletta, A., Molter, C., Duqué, R. & Steenhoff, D. Genome Biol. 13, R104 (2012).

    Article  Google Scholar 

  30. Frazee, A.C., Jaffe, A.E., Langmead, B. & Leek, J. bioRxiv http://biorxiv.org/content/biorxiv/early/2014/06/06/006015.full.pdf (2014)

    Google Scholar 

  31. Schroeder, A. et al. BMC Mol. Biol. 7, 3 (2006).

    Article  Google Scholar 

  32. Storey, J.D. et al. PNAS 102, 12837–12842 (2005).

    Article  CAS  Google Scholar 

  33. Paulson, J.N., Stine, O.C., Bravo, H.C. & Pop, M. Nat. Methods 10, 1200–1202 (2013).

    Article  CAS  Google Scholar 

  34. Price, A.L. et al. Nat. Genet. 38, 904–909 (2006).

    Article  CAS  Google Scholar 

  35. Leek, J.T. & Storey, J.D. PLoS Genet. 3, 1724–1735 (2007).

    Article  CAS  Google Scholar 

  36. Shabalin, A.A. Bioinformatics 28, 1353–1358 (2012).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors would like to thank P.A.C. 't Hoen and T. Lappalainen for providing QC data and assistance with contacting ArrayExpress. They would also like to acknowledge C. Trapnell for helpful conversations about Cufflinks architecture and results. J.T.L., G.P. and B.L. were partially supported by US National Institutes of Health 1R01GM105705, and A.C.F. is supported by a Hopkins Sommer Scholarship.

Author information

Authors and Affiliations

  1. Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA

    Alyssa C Frazee, Andrew E Jaffe, Ben Langmead, Steven L Salzberg & Jeffrey T Leek

  2. Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA

    Alyssa C Frazee, Geo Pertea, Andrew E Jaffe, Ben Langmead, Steven L Salzberg & Jeffrey T Leek

  3. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Geo Pertea & Steven L Salzberg

  4. Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland, USA

    Andrew E Jaffe

  5. Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA

    Ben Langmead & Steven L Salzberg

Authors
  1. Alyssa C Frazee
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Geo Pertea
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Andrew E Jaffe
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ben Langmead
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Steven L Salzberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jeffrey T Leek
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jeffrey T Leek.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary texts and figures

Supplementary Figures 1–10 and Supplementary Notes 1–11 (PDF 1618 kb)

Supplementary Information

Code to reproduce our analyses (ZIP 320952 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Frazee, A., Pertea, G., Jaffe, A. et al. Ballgown bridges the gap between transcriptome assembly and expression analysis. Nat Biotechnol 33, 243–246 (2015). https://doi.org/10.1038/nbt.3172

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt.3172

This article is cited by

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