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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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How to generate bed file from sql database #264

Closed m0nib closed 2 years ago

m0nib commented 2 years ago

Hi,

is it possible to construct or generate bed file or extract modified bases from the sql database, that is created as part of the megalodon pipeline?

We can start the liveprocessing with megalodon but our downstream pipeline analysis requires bed file.

Could provide instructions on how to achieve this?

thank you Monib

marcus1487 commented 2 years ago

The megalodon_extras aggregate run command will compute the bed file from the produced sql modified base data base. See docs here: https://nanoporetech.github.io/megalodon/extras_aggregate.html