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

ABSTRACT:

Unlabelled

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.

SUBMITTER: Akman K

PROVIDER: S-EPMC4071208 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature

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

Akman Kemal K Haaf Thomas T Gravina Silvia S Vijg Jan J Tresch Achim A

Bioinformatics (Oxford, England) 20140310 13

<h4>Unlabelled</h4>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 ge ...[more]

PMID: 24618468

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