Question about methylation location

Question

[Eren]

Hi, I am new to the analysis of methylation data, and I am confused about something. How do I get and visualize the methylated (not differentially, just in a sample) regions with their locations for WGBS data?

[dthorbur]

What data do you have? Generally, you start with sequencing data, which you need to clean and then map to a reference genome. Then depending on the tools you are using, you can generate a VCF or BED file with called mehtylation sites.