Base modification detection for direct RNA sequencing Nanopore

Question

[henry-keen]

We have Nanopore RNA sequencing data (fast5) generating using the RNA002 chemistry. We are interested in determining the methylation status (5mc) of these reads. At least initially, we don't even need to align the reads, we just want to know which reads show methylation.

Thanks for your help.

[GenoMax]

Do you know if this is possible to do? I don't see any methylation models for dorado (ONT basecaller) for RNA runs.

[henry-keen]

Thanks. I'm not sure. You're right, I don't see any model for RNA modifications on the dorado GitHub either.

Answer 1

[colindaven]

There might be something on this list for you. https://github.com/GoekeLab/awesome-nanopore

RNA has been rather neglected by Nanopore themselves, but there is a considerable amount of academic software for this. Check the pore and kit versions etc match since otherwise you will get poor predictions out.

[henry-keen]

I hadn't seen this list before. That's very helpful. Thank you very much.