In order to be able to better assess the relationship between TADs, the associated protein file (e.g. CTCF for mammals) can be included. The protein file is required in broadpeak forma

Optional parameter to adjust the number of protein peaks when adapting the resolution to the domain files. At least minimumNumberOfPeaks of unique peaks must be in a bin to considered. Otherwise the bin is treated like it has no peaks

Determine a value by how much the boundaries of two TADs must at least differ to consider them as two separate TADs

For the relationship determination, a percentage is required from which area coverage the TADs are related to each other. For example, a relationship should be entered from 5 percent area coverage