Hi, In HiC-Pro, it can automatically detect the valid pairs and remove Self circles. (https://github.com/nf-core/hic/blob/master/docs/output.md). And it has a --min_cis 1000 to remove short range contacts for DNase Hi-C (https://github.com/nf-core/hic/blob/master/docs/usage.md).
My data is using DpnII restriction enzymes. I find the treamtment Hi-C shows significant higher along the diagnoal in Hi-C map in treament than the control. The overall difference in two conidtions shoule be small in fact.
The significant increase in short range contacts along the diagnoal Hi-C looks not reasonable.
Hence, is it essential to filter diagonal short range contact (<=10kb) after HiC-Pro? Then after normalization, the difference along the diagnoal will be small because of most of them are removed.
Thanks very much.
