If my replicates are highly reproducible, is it valid to merge my replicates before finding peaks?
This is definitely an option for combining replicates. In fact, one paper indicates that merging replicates before peak calling improves the statistical power of your data. When deciding which stage to merge your replicate samples before peak calling, think about what deduplication method you are using and how that might affect your results. You also want to think about whether you are going to do differential peak calling on the data set as you will need to keep the replicates separate for differential peak calling if you want to have statistical power. – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.
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