How to separate "merged" chromosomes?

[ManuPoretti]

Hello, we find some discrepancies between our final polished genome assembly and cytogenetic map.
The main problem is that 3 chromosomes and several other genomic blocks (belonging to other chromosomes) are merged into one very large scaffold.
I tried several combinations of hicstuff parameters (different mapping software: bowtie2, bwa, minimap2; different mapping options: “iterative” or “cutsite”; the “duplicates” option to remove PCR artefacts), and finally run Instagraal using “-l 5” or “-l 5 -c 0” parameters. However, I always find this super scaffold.
Do you have any idea of what I could try to be more “stringent” and avoid that different chromosomes are merged together?
Thank you in advance!

[nadegeguiglielmoni]

Hello,

What parameter do you use for -e when running hicstuff pipeline? Would you mind sharing your contact map?

[ManuPoretti]

DpnII was used to digest the DNA, so I used -e DpnII.

You can download the contact map from the link below. It was generated using the parameters "-a bowtie2 -m iterative --duplicates -e DpnII".

https://www.swisstransfer.com/d/81380069-ea06-4cb9-8b79-d505bdaaab64

Thanks!