Recommended normalization procedure for CUT&Tag coverage file

Question

[Zain Arifin]

Hi!

I am performing CUT&Tag data analysis, and I am currently generating a coverage file using bamCoveragefrom the deepTools suite. For general best practice, what would be the best normalization method? I am currently using CPM but I am unsure if this is the best.

Any opinion would be very appreciated!

Many thanks!

Answer 1

[ATpoint]

My preference: ATAC-seq sample normalization

[Zain Arifin]

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.