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Oxford Nanopore's Basecaller
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Bases modified duplex basecalling #894

Closed angelluigi closed 1 week ago

angelluigi commented 1 week ago

Hello,

I suppose this is an easy question to answer but I have not been able to. I want to detect the 6mA in data obtained by nanopore.

This is the code I am running. dorado basecaller ../../dna_r10.4.1_e8.2_400bps_sup@v4.3.0 ../../barcode06.pod5 --modified-bases-models ./dorado_modelsres_dna_r10.4.1_e8.2_400bps_sup@v4.0.1_6mA@v2 > barcode05_v2.bam

It is not clear to me how to make the basecaller for duplex data, or if it is already doing it by default.

Best regards

malton-ont commented 1 week ago

Hi @angelluigi,

Info on duplex basecalling can be found here, but in summary, replace dorado basecaller with dorado duplex.

Also, you appear to be using a research model for the 6mA calling. Note that dorado has built-in 6mA models for sup@v4.3.0 named dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v2

angelluigi commented 1 week ago

Hi,

Ok, I'll check it out. I got the other model from remora. The one you are talking about, does it work better?

Thanks

[cid:94338633-0318-47cc-aeb2-ed6821a24b9b]

De: malton-ont @.> Enviado: martes, 18 de junio de 2024 10:15 Para: nanoporetech/dorado @.> Cc: ANGEL LUIGI GUARNIZO SERRUDO @.>; Mention @.> Asunto: Re: [nanoporetech/dorado] Bases modified duplex basecalling (Issue #894)

Hi @angelluigihttps://urldefense.com/v3/__https://github.com/angelluigi__;!!D9dNQwwGXtA!QSqkRbsBWH09RMgAYLrsmwMg7f1bmGPud6ACmGPL-durpck9A4POF0uAVV7nAeG-5NII3zCJCkyVRq4_LUO8gCs4a_8hk1I$,

Info on duplex basecalling can be found herehttps://urldefense.com/v3/__https://github.com/nanoporetech/dorado?tab=readme-ov-file*duplex__;Iw!!D9dNQwwGXtA!QSqkRbsBWH09RMgAYLrsmwMg7f1bmGPud6ACmGPL-durpck9A4POF0uAVV7nAeG-5NII3zCJCkyVRq4_LUO8gCs4OknEYxU$, but in summary, replace dorado basecaller with dorado duplex.

Also, you appear to be using a research model for the 6mA calling. Note that dorado has built-in 6mA models for @. named @*.**@*.***

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/nanoporetech/dorado/issues/894*issuecomment-2175486307__;Iw!!D9dNQwwGXtA!QSqkRbsBWH09RMgAYLrsmwMg7f1bmGPud6ACmGPL-durpck9A4POF0uAVV7nAeG-5NII3zCJCkyVRq4_LUO8gCs4IoFpdr0$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ALWFEHQQKCBFNGZ3FDJRHL3ZH7UCBAVCNFSM6AAAAABJPN5QKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNZVGQ4DMMZQG4__;!!D9dNQwwGXtA!QSqkRbsBWH09RMgAYLrsmwMg7f1bmGPud6ACmGPL-durpck9A4POF0uAVV7nAeG-5NII3zCJCkyVRq4_LUO8gCs4WFQz7I0$. You are receiving this because you were mentioned.Message ID: @.***>

malton-ont commented 1 week ago

@angelluigi,

Unless you have a pressing reason to use other models, we recommend the bundled ones.

angelluigi commented 1 week ago

Hi,

I have finally launched it like this: dorado duplex models/dna_r10.4.1_e8.2_400bps_hac@v4.3.0 barcode06.pod5 --modified-bases 6mA --reference CB5A.fasta > barcode06_v3.bam. You could do the same but with barcode01.pod5.

With this I got an error: dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v2