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nanoporetech / dorado

Oxford Nanopore's Basecaller
https://nanoporetech.com/
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Redo basecalling on both POD5_pass and fail folders #820

Closed Harper19 closed 1 month ago

Harper19 commented 1 month ago

Wanna redo HAC mode basecalling to obtain more useful data. How could I deal with those 2 folders? Should I directly combine them together into one folder?

Thanks, Harper

HalfPhoton commented 1 month ago

Hi @Harper19, Using the --recursive option you can either basecall the parent directory or a new directory with symbolic links to the two pass / fail folders.

dorado basecall hac . --recursive > calls.hac.bam
mkdir all_data
cd all_data
ln -s ../pod5_pass 
ln -s ../pod5_fail
cd .. 
dorado basecall hac all_data/ --recursive > calls.hac.bam

Kind regards, Rich

Harper19 commented 1 month ago

Thank you so much! -Harper