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aidenlab / straw

Extract data quickly from Juicebox via straw
MIT License
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Is there a way to extract the inter-balanced matrix or the genome-wide matrix? #113

Open mellofariam opened 2 years ago

mellofariam commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

What flavor/language are you working with?

mellofariam commented 2 years ago

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