Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data
Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data
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DOI：
10.1093/bioinformatics/btu142
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发表时间：
2014-07-01
期刊：
影响因子：
5.8
通讯作者：
Tresch, Achim
中科院分区：
文献类型：
--
作者：
Akman, Kemal;Haaf, Thomas;Tresch, Achim
在这里，我们介绍了开源R/BioConductor软件包BEAT(BS-Seq环境分析工具包)。它实现了从亚硫酸氢盐测序数据中对DNA甲基化模式进行定量高分辨率分析所需的所有生物信息学步骤，包括检测区域突变事件，即相对于参考的CG位置的DNA甲基化的丢失或增加。使用二项混合模型，BEAT程序包聚合了每个基因组位置的甲基化计数，从而补偿了低覆盖率、不完全转换和测序错误。可获得性和实施：BEAT作为BioConductor的一部分可在www.BEAT免费获得。生物导体。Org/Packages/devel/Bioc/html/Beat。HTML。该程序包在GNU宽松通用公共许可证3.0下分发。
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.