I am currently analyzing a MBD-seq data set for 14 tissue samples (7 each from groups A and B----each with individual controls). My main goals as of now is to identify any differentially methylated regions between the two groups and also to see if some or all samples from each group cluster together based on the methylation pattern of distinct genomic regions (e.g. CpG Islands in promoters etc). I have results from several pipelines MEDIPS, MACS, MAC2, DiffBind, Homer. I wanted to see what other groups currently use for this analysis. Any suggestions would be welcome. Also what would be best way to do groupwise comparison using 7 from each groups as replicates.