Work

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

Year: 2014

Type: article

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.

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btu142

Authors: Kemal Akman, Thomas Haaf, Silvia Gravina, Jan Vijg, Achim Tresch

Institutions: Albert Einstein College of Medicine, University of Würzburg, Max Planck Institute for Plant Breeding Research

Language: English

Topic: Epigenetics and DNA Methylation

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: bronze

Funders: Deutsche Forschungsgemeinschaft, Bundesministerium für Bildung und Forschung, National Institutes of Health, National Institute on Aging