I have recently started looking into how to analyze bisulfite sequencing data, which I am completely new to, and am hoping if someone here could provide some insights.
I work on a non-model species, and I have whole genome sequencing data of bisulfite converted DNA (WGBS), as well as whole genome sequencing of non-converted DNA (WGS) obtained from the same set of samples. The goal is to identify methylated regions by comparing these two types of data.
Does anyone know if there are any tools out there that consider both WGBS and WGS and infer methylated sites? As far as I know, many tools like Methylkit only consider only WGBS data, and I wasn't sure if this is something that is done by custom made scripts or if there are any existing tools out there I could use.
Many thanks in advance!