IDEAS home Printed from https://ideas.repec.org/a/plo/pcbi00/1003494.html
   My bibliography  Save this article

Universal Count Correction for High-Throughput Sequencing

Author

Listed:
  • Tatsunori B Hashimoto
  • Matthew D Edwards
  • David K Gifford

Abstract

We show that existing RNA-seq, DNase-seq, and ChIP-seq data exhibit overdispersed per-base read count distributions that are not matched to existing computational method assumptions. To compensate for this overdispersion we introduce a nonparametric and universal method for processing per-base sequencing read count data called Fixseq. We demonstrate that Fixseq substantially improves the performance of existing RNA-seq, DNase-seq, and ChIP-seq analysis tools when compared with existing alternatives.Author Summary: High-throughput DNA sequencing has been adapted to measure diverse biological state information including RNA expression, chromatin accessibility, and transcription factor binding to the genome. The accurate inference of biological mechanism from sequence counts requires a model of how sequence counts are distributed. We show that presently used sequence count distribution models are typically inaccurate and present a new method called Fixseq to process counts to more closely follow existing count models. On typical datasets Fixseq improves the performance of existing tools for RNA-seq, DNase-seq, and ChIP-seq, while yielding complementary additional gains in cases where domain-specific tools are available.

Suggested Citation

  • Tatsunori B Hashimoto & Matthew D Edwards & David K Gifford, 2014. "Universal Count Correction for High-Throughput Sequencing," PLOS Computational Biology, Public Library of Science, vol. 10(3), pages 1-11, March.
  • Handle: RePEc:plo:pcbi00:1003494
    DOI: 10.1371/journal.pcbi.1003494
    as

    Download full text from publisher

    File URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003494
    Download Restriction: no

    File URL: https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003494&type=printable
    Download Restriction: no

    File URL: https://libkey.io/10.1371/journal.pcbi.1003494?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Chang, George T. & Walther, Guenther, 2007. "Clustering with mixtures of log-concave distributions," Computational Statistics & Data Analysis, Elsevier, vol. 51(12), pages 6242-6251, August.
    2. Elizabeth G Wilbanks & Marc T Facciotti, 2010. "Evaluation of Algorithm Performance in ChIP-Seq Peak Detection," PLOS ONE, Public Library of Science, vol. 5(7), pages 1-12, July.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Madeleine Cule & Richard Samworth & Michael Stewart, 2010. "Maximum likelihood estimation of a multi‐dimensional log‐concave density," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 72(5), pages 545-607, November.
    2. Mu, Xiaosheng, 2015. "Log-concavity of a mixture of beta distributions," Statistics & Probability Letters, Elsevier, vol. 99(C), pages 125-130.
    3. Caiyan Jia & Matthew B Carson & Yang Wang & Youfang Lin & Hui Lu, 2014. "A New Exhaustive Method and Strategy for Finding Motifs in ChIP-Enriched Regions," PLOS ONE, Public Library of Science, vol. 9(1), pages 1-13, January.
    4. Anthony Mathelier & Wyeth W Wasserman, 2013. "The Next Generation of Transcription Factor Binding Site Prediction," PLOS Computational Biology, Public Library of Science, vol. 9(9), pages 1-18, September.
    5. Weronika Sikora-Wohlfeld & Marit Ackermann & Eleni G Christodoulou & Kalaimathy Singaravelu & Andreas Beyer, 2013. "Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data," PLOS Computational Biology, Public Library of Science, vol. 9(11), pages 1-11, November.
    6. Hazelton, Martin L., 2011. "Assessing log-concavity of multivariate densities," Statistics & Probability Letters, Elsevier, vol. 81(1), pages 121-125, January.
    7. Yuzhuo Wang & Chengzhi Zhang & Kai Li, 2022. "A review on method entities in the academic literature: extraction, evaluation, and application," Scientometrics, Springer;Akadémiai Kiadó, vol. 127(5), pages 2479-2520, May.
    8. repec:jss:jstsof:39:i06 is not listed on IDEAS
    9. Hu, Hao & Yao, Weixin & Wu, Yichao, 2017. "The robust EM-type algorithms for log-concave mixtures of regression models," Computational Statistics & Data Analysis, Elsevier, vol. 111(C), pages 14-26.
    10. Azadbakhsh, Mahdis & Jankowski, Hanna & Gao, Xin, 2014. "Computing confidence intervals for log-concave densities," Computational Statistics & Data Analysis, Elsevier, vol. 75(C), pages 248-264.
    11. Timothy Bailey & Pawel Krajewski & Istvan Ladunga & Celine Lefebvre & Qunhua Li & Tao Liu & Pedro Madrigal & Cenny Taslim & Jie Zhang, 2013. "Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data," PLOS Computational Biology, Public Library of Science, vol. 9(11), pages 1-8, November.
    12. Dongjun Chung & Dan Park & Kevin Myers & Jeffrey Grass & Patricia Kiley & Robert Landick & Sündüz Keleş, 2013. "dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data," PLOS Computational Biology, Public Library of Science, vol. 9(10), pages 1-13, October.
    13. Hu, Hao & Wu, Yichao & Yao, Weixin, 2016. "Maximum likelihood estimation of the mixture of log-concave densities," Computational Statistics & Data Analysis, Elsevier, vol. 101(C), pages 137-147.
    14. Apratim Mitra & Jiuzhou Song, 2012. "WaveSeq: A Novel Data-Driven Method of Detecting Histone Modification Enrichments Using Wavelets," PLOS ONE, Public Library of Science, vol. 7(9), pages 1-11, September.
    15. Haipeng Xing & Yifan Mo & Will Liao & Michael Q Zhang, 2012. "Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data," PLOS Computational Biology, Public Library of Science, vol. 8(7), pages 1-12, July.
    16. Arias-Castro, Ery & Pu, Xiao, 2019. "Concentration of measure for radial distributions and consequences for statistical modeling," Statistics & Probability Letters, Elsevier, vol. 145(C), pages 216-223.
    17. Balabdaoui, Fadoua & Butucea, Cristina, 2014. "On location mixtures with Pólya frequency components," Statistics & Probability Letters, Elsevier, vol. 95(C), pages 144-149.
    18. Wraith, Darren & Forbes, Florence, 2015. "Location and scale mixtures of Gaussians with flexible tail behaviour: Properties, inference and application to multivariate clustering," Computational Statistics & Data Analysis, Elsevier, vol. 90(C), pages 61-73.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pcbi00:1003494. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.