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Bioinformatics. 2014 Jul 1;30(13):1933-4. doi: 10.1093/bioinformatics/btu142. Epub 2014 Mar 10.

Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data.

Author information

1
Tresch Group, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany, AG Haaf, Institute of Human Genetics, Julius Maximilians University, 97070 Wuerzburg, Germany and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

Abstract

Here we present the open-source R/Bioconductor software package BEAT (BS-Seq Epimutation Analysis Toolkit). It implements all bioinformatics steps required for the quantitative high-resolution analysis of DNA methylation patterns from bisulfite sequencing data, including the detection of regional epimutation events, i.e. loss or gain of DNA methylation at CG positions relative to a reference. Using a binomial mixture model, the BEAT package aggregates methylation counts per genomic position, thereby compensating for low coverage, incomplete conversion and sequencing errors.

AVAILABILITY AND IMPLEMENTATION:

BEAT is freely available as part of Bioconductor at www.bioconductor.org/packages/devel/bioc/html/BEAT.html. The package is distributed under the GNU Lesser General Public License 3.0.

PMID:
24618468
PMCID:
PMC4071208
DOI:
10.1093/bioinformatics/btu142
[Indexed for MEDLINE]
Free PMC Article

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