Question about downscaling 10-kb matrix to 8192 bp resolution

[zhang-jiankun]

Hi @tanjimin ,

I really enjoyed using C.Origami, but I got a naive question that has been bothering me for a while. I was wondering how to downscale the 10-kb experimental Hi-C matrix to 8192 bp resolution in order to match the model outputs.

Best,

Jiankun

[tanjimin]

Hi Jiankun, this is the line where I performed transformation:

C.Origami/src/corigami/data/chromosome_dataset.py

Line 118 in d5619eb

mat = resize(mat, (self.image_scale, self.image_scale), anti_aliasing=True)

[zhang-jiankun]

Hi @tanjimin,

This is very clear. I would like to convert C.Origami prediction or even perturbed matrix to .cool file, and perform downstream analyses using the cooler package (https://cooler.readthedocs.io/en/latest/). Is it reasonable to resize the 256 x 256 output back to 210 x 210 and generate new cool file? I was also wondering if there is an implementation in the C.Origami repo.

Any advice would be greatly appreciated!

Best,

Jiankun

[tanjimin]

Yes, that is doable. This is also a feature I am currently working on: #24 although I don't have plan to include perturbed matrix. You can try to implement it and do a pull request!

[zhang-jiankun]

I got it. Thank you for your help!