Question about the preprocessing script bam_cov.py

calico / basenji

Sequential regulatory activity predictions with deep convolutional neural networks.

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Question about the preprocessing script bam_cov.py #195

Open whui2bioinformatics opened 4 months ago

whui2bioinformatics commented 4 months ago

Hi, It seems that the bam_cov.py script that converts bam file to bigwig file does not involve sequencing depth normalization. I need to compare the difference in predicted results between samples, but the predicted difference is consistent with the difference in sequencing depth!

davek44 commented 4 months ago

Correct, we do not perform depth normalization in that script. I generally perform normalization afterward on the model outputs.