HiC map refinement

[yiming wu]

Dear 3D Genomics members,

Thanks for providing us with this great tool and tutorials.

I have finished a genome assembly using 3D-dna based on contigs derived from hifiasm.

Here is my overall review of the hic map:

This is my first time doing genome assembly. Would you please give some suggestions on where to start to refine my hic contact map?

I have more concerns about the following two pseudochromosomes: 

I am not sure how to refine these two chromosomes, they have many mosaic-like stripes.

I feel that I need to do many translocation corrections, but I have to split the green scaffolds, my understanding is that we'd better keep the scaffolds rather than split them. Would you please give me some guidance here?

Thanks in advance!

Best regards,

Yiming

[Olga Dudchenko]

Yiming,

please consult the genome assembly cookbook (dnazoo.org/manual) for general guidance. The "mosaic" is a normal appearance and is a Hi-C manifestation of open/closed chromatin segregation.

Olga

[yiming wu]

Dear Olga,

Thanks for your reply. I will correct the obvious inversions, translocations, etc. following the cookbook guidance.

Best,

Yiming