How to plot scaling curves for Hi-C data?

Question

[Linus]

Hi all,

I've got some Hi-C data that I'm trying to analyze. However, being a wet-lab person, I have minimal experience whatsoever with bioinformatics. So far, I've got some paired-end Hi-C data which I've aligned to the genome, performed deduplication of reads and created contact matrices using tools like HiC-Pro and Cooler.

I want to create scaling curves which show the periodicity in the genome from about 100 bp, up to 2kb. Is there any tool out there that I can make use of to make such graphs?

Thanks

Answer 1

[Алёна Константиновна]

there's cooltools expected for that (https://cooltools.readthedocs.io/en/latest/notebooks/contacts_vs_distance.html)