jorisbalc

For both the custom modification and methylation model training we used two substrates. Both were ~1kb in lenght with a GC content of ~40%. Only the CpG sites were modified,...

Thank you for the reply. That's what we figured aswell. You also mentioned that a model differentiating two distinct modifications can be trained (similar to the mC/hmC model provided). Could...

The export function input is required to be a directory.

Hi marcus, I'm getting a similar issue with the newest dorado version (0.6.1) while trying to run `remora analyze plot ref_region` as written in the readme: ``` remora analyze plot...

Hi. Got some questions as well on that regard. Is it possible to run the remora tied basecalling models such as `[email protected]_5mCG_5hmCG `along custom remora models via --modified-bases-models? For the...

Thanks for the clarification. How do you avoid the `[error] Maximum number of positional arguments exceeded` when adding multiple models via --modified-bases-models? Also, should I be retraining my remora model...

@tijyojwad Forgot to add it with the post but here it is: ``` v313@v313-GP66-Leopard-11UH:~$ dorado basecaller /home/v313/Dorado/models/[email protected] /media/v313/T7\ Shield/2023_12_06_FAT_PL/bc14/ --modified-bases-models /home/v313/Dorado/models/[email protected]_5mCG_5hmCG@v1 /media/v313/Dorado/models/remora/odyC_v1.0/ --reference /home/v313/ref-seqs/gm119_ref.fasta > calls_mC_hmC_odyC.bam ``` This should work...

I'd assume this was addressed to me. The T7 Shield is just a storage device for some of the data. It is not the problem here since the whitespace escaped...

Correct, adding a second model after `--modified-bases-models ` treats it as third argument. Example: `dorado basecaller --modified-bases-models > calls.bam` works `dorado basecaller --modified-bases-models > calls.bam` does not work

Seems that I have overlooked this. Works fine now, thanks for the replies!