Presently I am working on Bisulfite sequencing data for three sample, After primary Analysis using the Bismark tool. I got a bedgraph output. The output bedgraph shows position wise methylation call and the read depth.
For the further Analysis, i wanted to know what should be a better procedure for studying Differential methylation.
Would it be wise choice if we first check the methylation call at different sites ( promoter-TSS, intergenic, exon and TTS). or if would it create a wrong interpretation as the methylation calls are position wise.
Would be thankful for your kind replies.