Identification of differentially methylated regions in the genome of Arabidopsis thaliana

DNA methylation profiling in the epigenome of Arabidopsis thaliana (Arabidopsis) has provided great insights in the role of this epigenetic mark for the regulation of transcription in plants, and is often based on high-throughput sequencing. The analysis of these data involves a series of steps including quality checks, filtering, alignment, identification of methyl-cytosines, and the identification of differentially methylated regions. This chapter outlines the computational methodology required to profile genome-wide differential methylation patterns based on publicly available Arabidopsis base-resolution bisulfite sequencing data. The methylPipe Bioconductor package is adopted for the identification of the differentially methylated regions, and all the steps from the raw data to the required input are described in detail.