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broadinstitute / ABC-Enhancer-Gene-Prediction

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
MIT License
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Apply ABC model to independent cell types #214

Closed NicoleYY77 closed 6 months ago

NicoleYY77 commented 7 months ago

Hi, I'm wondering that how could I apply this model on new cell type, for example, iPSCs? I can get Dnase-seq, H3K27ac data of iPSCs, and use the average Hi-C data as input, but for the normalization of Hi-C, it seems in need of a quantile reference file:

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so how should I get a reference file for iPSCs? really appreciate any help!

atancoder commented 6 months ago

You would want to keep the K562 reference file as is. https://abc-enhancer-gene-prediction.readthedocs.io/en/latest/usage/methods.html#quantile-normalization-for-activity