how to calibrate CTC-CRF model base qualities?

[lpryszcz]

Hi, how to calibrate bonito trained models so base qualities correspond to expected error rate?
For example config.toml for RNA004 sup models uses:

[qscore]
scale = 0.9
bias = -0.1

How were those values obtained?

[lpryszcz]

any update on this? we're in the review process of basecalling model trained with bonito and we are unable to calibrate qscores therefore qscores from CTC-CRF models are not comparable with older models (flip-flop).
I have opened similar issue in dorado repo

[yinshiyi]

I see your paper is accepted
https://pubmed.ncbi.nlm.nih.gov/39271295/
Congrats, did you figure it out at the end? Thanks