I have some primates HI-C data from NCBI GEO. I step-by-step followed HOMER Hi-C analysis pipeline to determine TADs and loops from the Hi-C reads. Theoretically, there are multiple loops in a TAD and number of loops are always higher than TADs. However, I got TADs in much higher number than loops.
Does someone have any idea why is it happening? Should I try using some tool other than HOMER for TAD and loop calling?