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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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gene expression input? #191

Closed olechnwin closed 8 months ago

olechnwin commented 8 months ago

Hi,

How do I specify the gene expression as input? Through out the paper, differential expression genes were mentioned and sound like they are used in the prediction model? But how do I specify it?

Thanks in advance for your help!

atancoder commented 8 months ago

ABC doesn't take gene expression as input. Maybe you're referring to the CRISPR dataset, or that we are comparing predictions to gene expression?

olechnwin commented 8 months ago

Thank you so much for your reply! I must have misunderstood the paper then. I also saw this issue and thought gene expression is one of the input #156 . Is this where you are comparing predictions to gene expression?

atancoder commented 8 months ago

in the context of that PR, we are interesting in making predictions only for genes that are expressed. We estimate a gene is expressed by looking at the accessibility at the promoter region, and making sure it meets a threshold. (we don't look at RNA-seq of any sort)