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

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

doi:10.1186/gb-2012-13-10-R83

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

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

Bloomberg School of Public Health

Research output: Contribution to journal › Article › peer-review

349 Scopus citations

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 language	English (US)
Article number	R83
Journal	Genome biology
Volume	13
Issue number	10
DOIs	https://doi.org/10.1186/gb-2012-13-10-R83
State	Published - Oct 3 2012

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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10.1186/gb-2012-13-10-R83

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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.",

author = "Hansen, {Kasper D.} and Benjamin Langmead and Irizarry, {Rafael A.}",

note = "Funding Information: This work was partially funded by HG004059 and P50HG003233. We thank Andrew P Feinberg for motivating the biological questions that led to the development of the analytical method; also for trusting us and running a large cancer experiment with 4× coverage. We thank Sarven Sabunciyan for helping us understand the technology, H{\'e}ctor Corrada-Bravo for discussions related to quality control and Margaret Taub for general comments and suggestions.",

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

Abstract

ASJC Scopus subject areas

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