High proportion of duplicates(%) in valid pairs

[miao zhang]

Hi nservant,

I am using HiC-Pro to process my HiC raw data. After alignment and filtering, I got some stats and pic to evaluate the quality of the datas, but that looks not that good compared with other published data. I listed some results and can you please help analyze whether this Hi-C data is successful?
1. the total percentage of aligned (76%~83%)
2. the percentage of  reported pairs (19.8%~32%); Not_reported pairs (61.5%~70.1%)
3. the perentage of valid interaction pairs (59.9%~73%); Invalid pairs (Dangling_end pairs 20.1%~31.2%)
4. the percentage of duplicates (56%~78%)

Thanks alot