Abstract
Here, we present BAT, a modular bisulfite analysis toolkit, that facilitates the analysis of bisulfite sequencing data. It covers the essential analysis steps of read alignment, quality control, extraction of methylation information, and calling of differentially methylated regions, as well as biologically relevant downstream analyses, such as data integration with gene expression, histone modification data, or transcription factor binding site annotation.
Highlights
High-throughput DNA methylation sequencing protocols, such as whole-genome bisulfite sequencing (WGBS) and targeted bisulfite sequencing (e. g., RRBS), have made it possible to precisely and accurately measure this major epigenetic modification on a genome wide scale
A number of time consuming data analysis steps are required in virtually all these projects, i. e., quality control, read alignment, and methylation rate calculation
It is designed to facilitate the analysis for biologists and physicians with little bioinformatic knowledge, as well as for bioinformaticians that already work on sequencing data, but are not familiar with the characteristics of bisulfite sequencing data
Summary
High-throughput DNA methylation sequencing protocols, such as whole-genome bisulfite sequencing (WGBS) and targeted bisulfite sequencing (e. g., RRBS), have made it possible to precisely and accurately measure this major epigenetic modification on a genome wide scale. High-throughput DNA methylation sequencing protocols, such as whole-genome bisulfite sequencing (WGBS) and targeted bisulfite sequencing Methylomes of a large number of samples have been sequenced in the context of cancer projects and developmental studies[1,2,3,4,5]. A number of time consuming data analysis steps are required in virtually all these projects, i. E., quality control, read alignment, and methylation rate calculation. Performing each step by hand is highly error prone, takes time, and impacts reproducibility. To ensure a consistent and reproducible processing, we have developed the Bisulfite Analysis Tooklit BAT. The workflow enables a fast and easy analysis of bisulfite converted high-throughput sequencing reads. It is designed to facilitate the analysis for biologists and physicians with little bioinformatic knowledge, as well as for bioinformaticians that already work on sequencing data, but are not familiar with the characteristics of bisulfite sequencing data
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