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!
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!