Base modification detection for direct RNA sequencing Nanopore
1
0
Entering edit mode
5 months ago
henry-keen ▴ 40

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 • 629 views
ADD COMMENT
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
5 months ago

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1452 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6