AlineMuyle

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running megalodon with all context DNA methylation models

Could you please explain what you mean by the latest Remora all-context model ? I just reinstalled remora and the following command line 'remora model list_pretrained' only shows CG models.

running megalodon with all context DNA methylation models

I think I found it! https://github.com/nanoporetech/rerio#remora-models Thank you for your help

updated pipeline relying on pod5 file format?

Thank you @PengNi I will keep an eye on your updates!

updated pipeline relying on pod5 file format?

Hi @PengNi I was wondering if you have any news on the updated pipeline with pod5/slow5? My datasets are very large and it would be super useful. Thank you for...

updated pipeline relying on pod5 file format?

Hi @PengNi thank you for the development of deepsignal3, I was wondering if models trained on R9 data will still work in deepsignal3? I would like to use it on...

updated pipeline relying on pod5 file format?

@PengNi Great! Thank you for the update.

pod5/slow5 support

Dear Dr Peng, I was wondering if you are considering updating your deepsignal-plant pipeline with the new compressed pod5 format? Including the resquiggle step. That would be extremely useful because...

Is option --n-ceil for reads only or also reference?

Thank you for your answer. So if I understand there is no threshold on the number of Ns in the reference, as long as the associated penalty does not affect...