Assistance with Hi-C contact map interpretation

[Guy Horev]

Hi,

I hope I don't start a redundant conversation,  I don't see my 1st message.

I am working on de novo genome of a plant that has 6 chromosome pairs (2n=12).

I did assembly with hifiasm and scaffolding with yahs.

I am trying to figure out if the resulting hic contact map is reasonable.

I particular I have two concerns:

The upper left joint looks strange to me, it also seems to be in proximity with what is currently defined as chromosome 5. Does it look like translocation? there is no clear bowtie shape like the cookbook example.

Should the two small chromosomes 6 and 7 be merged to one chromosome?

Are there other problems I am missing?

I would greatly appreciate your discussion.

Guy