E2G analysis at 2500kb using Alphagenome

Help & Support
1

Hi AlphaGenome Team,

Thank you for your excellent work!

I’m interested in Figure 4j of your manuscript. In this figure, I noticed that one of the bars shows a distance of 2500 kbp, which exceeds AlphaGenome’s maximum input length. Could you please explain how this was achieved?

Thank you!

1 Like
2

Hello,

Thank you for reaching out. The dataset itself has variants at 2.5 MB away, but we fail to predict them so assign 0.

The code for running this benchmark is here: https://github.com/karbalayghareh/ENCODE-E2G/blob/main/demo.ipynb, from the original authors. However, this doesn’t include AlphaGenome.