Predicted ALT expression and the REF expression separately

Help & Support
1

Hi,

When performing variant scoring for RNA-seq, the output includes raw_score a representation of the difference between ALT and REF alleles. Would AlphaGenome allow me to extract the predicted expression levels for the ALT and REF alleles separately, rather than just the aggregated score?

Thank you.

2

Hi There!

Thanks for reaching out.

Yes, you can extract them separately. While the score_variant function is optimized to return the aggregated difference (raw score), you should use the predict_variant function to access the individual predictions for each allele.

The predict_variant function returns an output object that contains separate reference and alternate fields (e.g., variant_output.reference.rna_seq and variant_output.alternate.rna_seq). This allows you to access and visualize the raw predicted expression tracks for the Reference (REF) and Alternate (ALT) alleles independently.

Some examples of using predict_variant can be found in our colab here: AlphaGenome - Visualizing predictions