Issue #34 new
I am a novice to capture hic analysis. We found that when we use hicpro or hicup for calling valid pairs from capture data, we found significant difference in output we get for chicago. can you explain why this should happen and what is more reliable method to move ahead. ?
Unfortunately, I am not familiar with HiC Pro - presumably, the count matrices are different between the two HiC alignment packages. We have always used HiCUP. Trans-interactions can be called as significant by design under very stringent criteria. Whether or not you wish to use them in downstream analyses depends on your specific question.