BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

Kasper D. Hansen, Benjamin Langmead, Rafael A. Irizarry

Research output: Contribution to journalArticlepeer-review

Abstract

DNA methylation is an important epigenetic modification involved in gene regulation, which can now be measured using whole-genome bisulfite sequencing. However, cost, complexity of the data, and lack of comprehensive analytical tools are major challenges that keep this technology from becoming widely applied. Here we present BSmooth, an alignment, quality control and analysis pipeline that provides accurate and precise results even with low coverage data, appropriately handling biological replicates. BSmooth is open source software, and can be downloaded from http://rafalab.jhsph.edu/bsmooth.

Original languageEnglish (US)
Article numberR83
JournalGenome biology
Volume13
Issue number10
DOIs
StatePublished - Oct 3 2012

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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