I have identified DEGs and interested to know methylation effect if so during evolution. We performed WGBS sequencing and extracted gene of interest and performed bismark methyl extract to the output specific region BAM file. I have attached the output but confused why it shows CpG methylation over the whole region when the gene is expressed and confirmed. I have some understanding to methylation analysis hence need some direction if I am doing wrong or what need to done.
Also,How can we identify promoter region from for the identified genes. I will be grateful to you all for your key inputs.