I have the following [from different published sources]:
1) [Protein of Interest] TF binding data at different time points in development (ChIP)
2) Histone modifications at different time points in development (ChIP)
3) Other proteins binding data that are enriched from MEME with (1) (ChIP)
I would like to see if the bound sites of (1) relate to (2) and (3).
Question A) Is there a simple designed pipeline for this?
Question B) How would you find % enrichment at (1) sites. As in H3K4me is enriched at 60% of (1) sites. Would you do a BED vs. BED of the binding peaks and see how many of them relate to each other or is there another better tool?