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nanoporetech / dorado

Oxford Nanopore's Basecaller
https://nanoporetech.com/
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base modifications for mRNA #853

Closed yul96 closed 4 months ago

yul96 commented 4 months ago

Hi Dorado team,

I have two questions about the mRNA modifications in the new dorado release 0.7

  1. For the pseU modification, is it for pseudouridine or N1-methylpseudouridine?

  2. Is it possible to call multiple base modifications in one run? I have tried "--modified-bases m6A,pseU" and it gives me errors on the syntax.

Thank you for the great work!

tijyojwad commented 4 months ago

For the pseU modification, is it for pseudouridine or N1-methylpseudouridine?

pseudouridine

Is it possible to call multiple base modifications in one run?

yes, please try --modified-bases pseU m6A instead

For future reference, please fill out the issue template along with the relevant details (full cmdline, exact error you see, etc.)

yul96 commented 3 months ago

@tijyojwad Thank you, the switch --modified-bases pseU m6A worked.

Do you have any timeline to make dorado work for the N1-methylpseudouridine modification in mRNA?

thanks

susie-ont commented 3 months ago

Hi @yul96 - we don't currently have a timeline for adding a modification model for N1-methylpseudouridine into Dorado, but we are working on a limited commercial release of a basecalling model for 100% modified N1-methylpseudouridine transcripts. If this is of interest then please get in touch with support@nanoporetech.com with more details of your use case and we can look into options.