Fragmented scaffolds - large and repetitive genome

[sighe]

Hi. We have got a 3d-dna output using 30x HiFi data and in-house Hi-C for a large, highly repetitive genome of about 5Gb, shown in a contact map on Juicebox like this.

We see 1) a huge fraction for which we could not retrieve chromatin contact and 2) a number of signals far away from the diagonal line, that is, fragments that failed to be resolved into chromosomal scaffolds. I expect that at least the fractions 2) can be better resolved into chromosomal scaffolds by tweaking with parameters. Any recommendations?

I would really appreciate your response.

Best regards.

[dudcha]

Hi,

Closing since this is not a bug report. Please consider reposting in Aidenlab.org/forum.html.

Thanks!
Olga