Transform old?

[watiss]

Hi,

I used the download_models.sh script to download the 4 replicates of the borzoi fold3 pre-trained model. Could you confirm if this was fit to data that was transformed using the transform_old option (like in this Makefile)? I wasn't sure how to find out from just the model files.

Thanks!
Best,
Valeh

[davek44]

Hi Valeh, sorry I lost track of this question. Yes, the data was transformed as you stated.

[nkempynck]

To add to this, in Borzoi Prime there is the notion of adding +1 to coverage values. This is implemented in the 'new' transforms. Yet, the targets files for Borzoi Prime also contain 'sum_sqrt' for RNA tracks, which in the new transforms should be 'sum_exp75' to follow the formula in the methods section. Am I correct in this? Was the old transform also used here?

Thanks a lot!
Niklas

[davek44]

Borzoi Prime used the exact same original transforms as Borzoi.