Is there a way to extract the inter-balanced matrix or the genome-wide matrix?

[mellofariam]

Reading the documentation I could not find any reference to those normalization procedures. I wonder if there is a way of using them.

Also, when an inter-chromosomal map is extracted with the balanced norm, which of the following procedures (if any) is used: inter-balancing or genome-wide balancing?

[sa501428]

If the file includes these normalizations, then yes. Just use INTER_KR or INTER_SCALE for the inter-balancing or GW_KR or GW_SCALE for genome-wide balancing. If you call it with KR or SCALE, it will use the intra-chromosomal balancing for the 2 chromosomes involved.

If the file doesn't include the normalizations, you'll want to balance the matrices with addnorm.

[sa501428]

What flavor/language are you working with?

[mellofariam]

I'm working with Python. I'll try that out! Thank you!