Does anyone have any ideas on how to run a control/input sample for a ChIP-exo experiment? Is it even necessary to run a control (similar to input DNA for ChIP-seq)? I'm looking for any references or forums that discuss this issue and experimental design?
This video (https://www.youtube.com/watch?v=8qLRI9Bqtso) briefly touches on this issue (t=32.45), indicating NOT to use an Input sample due to the Exo digestion. However, I don't know how the community (or reviewers) feel about this?
Thanks for any help!