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tanjimin / C.Origami

C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
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Training and prediction at 5kb resolution #46

Closed zhang-jiankun closed 2 months ago

zhang-jiankun commented 2 months ago

Hi @tanjimin ,

I would like to perform training and prediction at 5kb resolution. I have made the following changes in the code:

self.res = 5000 # 5kb resolution self.bins = 104.8576 # 104.8576 bins 1048576 bp self.image_scale = 128 # IMPORTANT, scale 105 to 128

I was wondering if this is enough. Are there any other things I should pay attention to?

tanjimin commented 2 months ago

Hi @zhang-jiankun these are reasonable edits. I think you also need to process your Hi-C data at 5kb resolution. There might be other small places that require modification. The quickest way to check would be printing the dimension of the input and inspecting target data as images from your edited dataloader.

zhang-jiankun commented 2 months ago

Thank you so much!