Analyzing WGBS data to identify DMRs without distinguishing between (CG, CHH, CHG)

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Hi Alex,

I am currently analyzing a batch of WGBS data on Arabidopsis thaliana. My goal is to identify DMRs without distinguishing between CG, CHH, and CHG, and to plot box plots showing the methylation rate distribution of CHH, CG, and CHG within the DMRs. When using methRead to read the CX_genome.txt file, it seems that the context must be chosen from one of the three. I would like to ask if I can select CG, CHH, or CHG for the context if my input CX_genome.txt file contains CHH, CG, and CHG.

I will appreciate your suggestions or explanations.

Thank you

Best,

Shen Yan