Signal tracks were generated for each replicate using deepTools [29]. For sharp signal data, scaling factors were estimated with the signal extraction scaling (SES) option, and further log2 ratios of ChIP over input signal were computed [30]. Broad signal data were scaled according to the total number of reads and again log2 ratios were calculated.
* see https://github.com/fidelram/deepTools/wiki/All-command-line-options#bamCompare
