Hello!
I am trying to assess the binding dynamics of two transcription factors that regulate macrophage responses in humans. I know that upon certain cytokine stimulations, there is a big binding overlap between the two TFs across the genome. The predicted binding motifs are also very similar. I would like to know in these shared TF peaks which one is preferentially bound or whether they bind with similar intensities. In this case normalization seems trivial since the global binding intensities between them may vary significantly. Does anyone have experience with this? What would be the best practices/tools to assess differential binding at shared sites?
I know MAnorm for example uses the common peaks between samples to derive a linear model that is then applied across all peaks, but does that account for global binding intensities?
I appreciate any helpful discussion on this!
