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tariks / peakachu

Genome-wide contact analysis using sklearn
MIT License
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diffPeakachu with newer models #18

Open ViriyaK opened 1 year ago

ViriyaK commented 1 year ago

Hello,

I was trying to use diffPeakachu to find differential loops between two conditions but I see that pair-probs.py is currently specifically mentioning the CTCF and H3K27ac trained models. I had called loops using the new high confidence models and wondering how I should proceed.

Also, your links to some of the models from github currently does not work.

Thanks!

Hendricks27 commented 1 year ago

I had the same question here actually...

XiaoTaoWang commented 1 year ago

Hi all, I have updated the README file, so that all links work. However, the script under the diffPeakachu folder was uploaded only for reproducing a figure in our original paper, and is not compatible with newer models trained with peakachu version >=2.0. Sorry for the inconvenience.

XiaoTaoWang commented 1 year ago

There are actually many ways to identify differential loops based on peakachu predictions. For example, a pixel can be defined as a differential loop if its peakachu score in one sample is greater than 0.9, but lower than 0.5 in the other sample.

Hendricks27 commented 1 year ago

Hey Dr. Wang,

Thank you so much for your detailed reply. It definitely clarifies a lot! For differential loop calling, is there a performance difference between the threshold method (which you just mentioned) and the gaussian mixture model? Thanks!