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Base modification detection for direct RNA sequencing Nanopore

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.

nanopore
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written by henry-keen • henry-keen

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

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written by GenoMax GenoMax

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

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written by henry-keen • henry-keen

1 answer

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.

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written by colindaven colindaven

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

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written by henry-keen • henry-keen

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