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BioMed Central, Genome Biology, 10(13), p. R83

DOI: 10.1186/gb-2012-13-10-r83

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

Journal article published in 2012 by Kasper D. Hansen ORCID, Benjamin Langmead, Rafael A. Irizarry
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Postprint: archiving allowed
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Data provided by SHERPA/RoMEO

Abstract

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 .