Regarding biological replicates in DNA methylation analysis
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?
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