What's default way to call 5mC only in Remora?

nanoporetech / megalodon

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.

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What's default way to call 5mC only in Remora? #248

Closed liuyang2006 closed 2 years ago

liuyang2006 commented 2 years ago

Hi, I am going to call 5mC vs. 5C, without concerning of 5hmC. Would you please confirm if my script below is the default model for Remora? Thank you!

megalodon \
    raw_fast5s/ \
    --guppy-config dna_r9.4.1_450bps_fast.cfg \
    --remora-modified-bases dna_r9.4.1_e8 fast 0.0.0 5mc CG 0 \
    --outputs basecalls mappings mod_mappings mods \
    --reference reference.fa \
    --devices 0 1 \
    --processes 20

marcus1487 commented 2 years ago

Yes. This is the recommended command to run remora within megalodon.