Hi ATpoint, many thanks for the feedback. It worked well for CUT&Tag data, where I have the same replicates of differing read depths. Typical normalization fails to account for this, but the use of TMM normalization does.

Quick question. Aside from visual examination, is there a metric that can be used to determine the similarity between coverage files? As in, how can we objectively quantify that this method performs better than the other? Thanks.