Dear all,

I need help regarding HpaII based DNA methylated seq data analysis since I am facing this kind of data first time. I have this data from liver cancer cell line with eight conditions and each conditions having three replicates. the aims of the study are to represent methylome profile of treated (with inhibitor) and untreated cell, then integrate this data with gene expression results and finally find some biomarkers that can assess this inhibitor . Please let me know, how to work this kind of data?

Thanks in advance

Rahul