High align rate but Low reported pairs

[hcph]

Dear HiCExplorer Team,

Thank you for this excellent tool. My Hi-C data analysis shows unusually low valid interaction pairs (see QC report below). Could you please offer some troubleshooting advice?

[joachimwolff]

Hi,

are you sure this is HiCExplorer? Our QC reports look quite different. It is new to me we report i.e. Pairs with singletons.

Besides this, I assume 'Duplicates' shall be PCR duplicates and a rate of 34% is not good. Try to get this down to 10%. Is your library saturated? 21% Trans Contacts (I assume these shall be inter chromosomal ones?) is also not a great value, should be lower. Maybe try to stabilize the cells that we don't get random inter-cell contacts in the fixation step.

Best,

Joachim