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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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The pre-trained models of other cell types #32

Open lhy0322 opened 11 months ago

lhy0322 commented 11 months ago

Dear Jimin, Your research has been very helpful in my work! I am trying to reproduce the best results of your method as our baseline to compare. Does Origami provide pre trained models for other cell types? (excluding IMR90)

thanks！

tanjimin commented 11 months ago

Hi @lhy0322 , sorry for the late reply. The idea of C.Origami is that the model trained on IMR-90 will also work on different cell types as well as shown in the paper. You can preprocess the ATAC-seq and CTCF ChIP-seq from other cell types and try the model directly.

May-0707 commented 2 months ago

Dear Jimin, I preprocessed the ATAC-seq and CTCF CUT&Tag from mm10 and try the model. The default epoch paramater is 80. The model saved at epoch=79-step=41760.ckpt does not produce any graphical results, whereas the model at epoch=0-step=522.ckpt can generate some graphs, though it is still far inferior to your pre-trained model. The email I sent you described the picture in detail. HiC-pro and hicpro2higlass.sh generated mcool, cool2npy.py change it to npz. CUT&Tag preprocessed with https://yezhengstat.github.io/CUTTag_tutorial/. Can you give me some suggestions for improvement or just use your pre-traind model ? Best regards, May Young