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Universal Count Correction for High-Throughput Sequencing

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  • 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
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    References listed on IDEAS

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    1. 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.
    2. 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.
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