allotetraploid genome with HiC

[mictadlo]

Hi,
I would like to try hickit with an allotetraploid denovo plant genome with HiC. It appears that HiC data has replicates because all my files looks this:

ls -1 /HiC
N_Ben_HiC2.R1.fq.gz
N_Ben_HiC2.R2.fq.gz
N_Ben_HiC4.R1.fq.gz
N_Ben_HiC4.R2.fq.gz

Do you think I would be able to get the expected 19 chromosome bins (19 FASTA files) for my genome?

If it is possible to use hickit then could you please help me what would I need to change in the mapping steps in your pipeline?

Or do you have a better solution how to extract 19 chromosome bins (19 FASTA files) out of a denovo plant genome assembly without any annotation?

Thank you in advance,

MIchal