Meaning of the test data's result from kipoi about basenji HOT 4 CLOSED

Questions about Kipoi output are best directed to the leaders of that project; I’m not familiar with how they’re using Basenji.

For predictions relative to a gene annotation, see this tutorial https://github.com/calico/basenji/blob/master/tutorials/genes.ipynb

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thanks for your reply. I have tried the GitHub basenji prediction with basenji_sed.py. It successfully gave me the expression results. However, I'm not sure what's the definition of gene expression. I'm curious that in the publication it seems the training results are the 128 bin coverage for different cell types. So how does basenji link the coverage with the expression? Does this method use TSS coverage to predict the expression? I suppose here the gene expression level is not the FPKM score.

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Yes, it’s using predicted activity in the 128 bp bin that covers the gene’s TSSs to describe its expression. I have a preprocessing step that takes in a GTF to determine those positions.

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Thank you for the explanation.

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