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nanoporetech / dorado

Oxford Nanopore's Basecaller
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All context 5mC model 5kHz in dorado #678

Closed jasmatth closed 5 months ago

jasmatth commented 6 months ago

Input code: dorado basecaller res_dna_r10.4.1_e8.2_400bps_sup@v4.0.1 pod5_directory --modified-bases-models res_dna_r10.4.1_e8.2_400bps_sup@v4.0.1_5mC@v2 > output.bam

When running this code I get following error: [error] Sample rate for model (4000) and data (5000) are not compatible.

I know this is related to the fact that the model is in 4kHz and the data is in 5kHz, but there is no model for all context 5mC in 5kHz. Are there any suggestions on how to deal with this issue?

HalfPhoton commented 6 months ago

Hi @jasmatth, The dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mC_5hmC@v1 is both a 5mC and 5hmC all-context model for 5kHz data. You should be able to run this with:

dorado basecaller sup,5mC_5hmC pod5_directory > output.bam

Kind regards, Rich

HalfPhoton commented 5 months ago

@jasmatth, has this answered your question?

jasmatth commented 5 months ago

Hi, yes, thanks for the help!