Regarding biological replicates in DNA methylation analysis

Question

[kajol21bm]

I am new to the NGS analysis field and have started learning analysis of Whole Genome Bisulphite Sequencing Data. I have two biological replicates for each of my sample. Some sample replicates have more than 5% difference in Mapping Efficiency. What difference in % mapping efficiency among the biological replicates is allowed? Also, what is the best way to proceed for further analysis: like pooling of biological replicates (in methylkit for DMR finding) or proceeding separately with each replicates and using logistic regression for DMR finding?

[ATpoint]

If you want to do any statistical analysis then you must not just merge them, use dedicatedtools such as How to do DMR analysis with BiSeq (for RRBS methylation data)?