Recommendations for huge HiC matrices

[V-JJ]

Good evening!

I would like to ask for some recommendations to work with huge HiC matrices corresponding to scaffolds ~100 Mb in size.
What I tried to do so far is the following :

• Define windows of 10 Mb (for example). That would imply 10 windows of 10 Mb for a chr of ~100 Mb
• Obtain the corresponding submatrices at a given resolution (for ex: 50 kb).
• Predict centromeres for each of the submatrices.

Is this correct? Or would you suggest some alternative solutions?

Many thanks,