• Methods Mol. Biol. · Jan 2017

    Computational Analysis of Genome-Wide ARGONAUTE-Dependent DNA Methylation in Plants.

    • Kai Tang, Cheng-Guo Duan, Huiming Zhang, and Jian-Kang Zhu.
    • Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China. tang58@purdue.edu.
    • Methods Mol. Biol. 2017 Jan 1; 1640: 219-225.

    AbstractWhole-genome bisulfite sequencing (WGBS) has become a powerful tool to dissect genome-wide methylation profiles at single-base resolution. In this chapter we describe in detail the bioinformatics pipeline used for the analysis of ARGONAUTE-dependent DNA methylation in Arabidopsis thaliana. We provide tools and command lines used for mapping bisulfite sequencing reads, for estimating methylation levels at individual cytosine sites, for identifying differentially methylated regions (DMRs), and for calculating methylation levels of DMRs.

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