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bernardo-de-almeida / DeepSTARR

Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Drosophila melanogaster S2 cells
MIT License
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how to make figure 1A #4

Closed BenxiaHu closed 1 year ago

BenxiaHu commented 1 year ago

Hello, The DeepSTARR looks a great tool to predict enhancer activity from DNA sequences. Would you like to tell me whether DeepSTARR can predict the motif from gene promoters? I also want to plot the figure 1A.

image
bernardo-de-almeida commented 1 year ago

Hi, The DeepSTARR model was trained on enhancer sequences so it is not a good model to evaluate promoter sequences. What you want would be possible if you train a DeepSTARR-like model on promoter activity data (or maybe DNA accessibility data that is more common and should work well) and then use that new model to evaluate promoters in a similar way as I do here. Hope it helps!