HiCKRy.py generated extreme bias value

[QianzhaoJ]

Hi:
When I tried to calculate bias values using HiCKRy.py, I found there are some extreme values as like chr1 30875000 2043.101940700636 ; but the bias file generated by ICE normalization using HiCPro is normal, chr1 30875000 0.8739076476642095. My script is simple : python $KR -i $in -f $frag -o $bias
Meanwhile when I used the bias file generated by HiCKRy.py to finding inter-chromosomal significant interactions, I obtained too much interactions (5183320,q<0.01), but when I used ICE normalized bias file, I only obtained some interactions (493135,q<0.01).
It seems that the inter-chromosomal significant interactions from ICE normalization were more solid through comapred with contact heatmap using juicer.
Maybe I should choose the ICE normalization for calling inter-chromosomal significant interactions. Counld you give me some suggestions?

Best wishes
Qianzhao

[ay-lab]

Hi Qianzhao,
There may be some stability issues with HiCKRy in some cases. This may be the case. Choosing to go with ICE or another KR implementation is logical.