How does Modkit handle long-read methylation 3D genomic data

[biozzq]

Dear @ALL

I think this question would be more appropriate here, so I referenced it here (nanoporetech/dorado#1089)

Thank you for your time.

Kind regards
Zheng zhuqing

[ArtRand]

Hello @biozzq,

There is documentation regarding how to use non-primary alignments in some of the modkit commands. However, as of now pileup does not aggregate non-primary alignments. It's not impossible by any means, but there are some sharp edges so I want to make sure it works correctly first. Are you looking for something like pore-c?