After multiple rounds of nanopore sequencing we have reached to 50-60 Gbases data for each sample. Pore-C run results in ~250 million contacts each. However downstream processing with juicer results in warning "Warning: Hi-C map is too sparse to find many domains via Arrowhead".
slurm-28491.txt
Also, similar warnings for HiCCUPS
Could you please suggest the minimum number of contacts required for a reliable pore-C analysis and how much data it would correspond to.
eharr
commented
3 years ago
Hello Eoghan and team,
After multiple rounds of nanopore sequencing we have reached to 50-60 Gbases data for each sample. Pore-C run results in ~250 million contacts each. However downstream processing with juicer results in warning "Warning: Hi-C map is too sparse to find many domains via Arrowhead". slurm-28491.txt
Also, similar warnings for HiCCUPS Could you please suggest the minimum number of contacts required for a reliable pore-C analysis and how much data it would correspond to.
Thanks Ant