Clarification on --model parameter in modkit open-chromatin predict

[DexinYang1998]

Hi,

Thank you for developing such a powerful and user-friendly tool!

I’m currently working on open chromatin prediction using modkit and had a question regarding the --model parameter in the open-chromatin predict command. Is this model the same as the one used by Dorado for base or modification calling, or is it an independent model specifically trained for chromatin accessibility?

If it is a separate model, could you please let me know where I can download it?

Thanks again for your great work!

[ArtRand]

Hello @DexinYang1998,

The model can be downloaded with one of the 0.5.0 modkit releases. They all have the same model in the models/ directory. Currently there is only one model, trained on High-Accuracy v5.2 data, but it should work fine with Super-High-Accuracy basecalls as well. There is a description of which build should be used in this issue.

The open-chromatin feature is new, so I'm keen to hear any feedback you may have.