I tried to run a small workflow on Galaxy, which basically attempts to establish a correlation between the Chip-Chip, Polymerase binding and Dnase Hypersensitivity data. The input would be these 3 files, I am initially performing a liftover on the Chip-Chip data to convert from hg18 to hg19 and then using the output to establish the correlation. Here, you can see a screenshot of the pipeline here: