In my lab we were interested in comparing a ChIPmentation experiment for a transcription factor (TF) A we performed some time ago (2-3 years), with a ChIPmentation experiment for TF B we still need to perform. The two TFs might interact with each other to perform their function and they also might be redundant in their function (e.g. direct targets). We are very hesitant if we need to recapitulate the conditions of the sequencing for TF A. This means that we would need to perform the sequencing for TF B: 50bp single-end reads and 20 M reads. I would like to ask to the community from my lack of knowledge if this is necessary / is it the best practices to compare the two experiments or it will not affect whatsoever the comparison given that the two experiments have their own inputs as control.