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MiraldiLab / maxATAC

Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
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Question about training/testing celltypes #116

Closed ninashenker closed 1 year ago

ninashenker commented 1 year ago

Hi maxATAC team.

Really awesome work!! Is there anyway to know what cell types were trained and tested on for each transcription factor? Specifically- I am interested in using your model to predict CTCF in GM12878 and IMR-90 to then predict Hi-C. I wanted to compared your predicted CTCF to CTCF Chip-seq. Was the CTCF model trained on those cell types?

Best, Nina

Update: I found the excel from the publication!

tacazares commented 1 year ago

Hello, The final models available are trained using all cell types. We did perform "round-robin" training as well (leave 1 cell type out and use the rest for training). We have models available for CTCF that excluded GM12878 or IMR-90 during training. If you are interested we could provide the h5 files for prediction. Thanks for your interest and we are interested in seeing your results! Tareian