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hasindu2008 / f5c

Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)
https://hasindu2008.github.io/f5c/docs/overview
MIT License
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recommended threshold for the log likelihood ratio #129

Open PengNi opened 1 year ago

PengNi commented 1 year ago

Hi @hasindu2008 and all,

For the f5c meth-freq step, is the reommended threshold for the log likelihood ratio still 2.5, or should be 2.0 as nanopolish has changed?

Thank you in advance!

Best, Peng

hasindu2008 commented 1 year ago

Hi

For f5c meth-freq, I have not implemented this scaling based on the group size discussed here https://github.com/jts/nanopolish/issues/695. That lowering of llr to 2.0 is only suitable if that group scaling is implemented as I understand.

What kind of data are you working on? R9 or R10?

PengNi commented 1 year ago

Hi @hasindu2008 , I am using R9.4.1 reads.

hasindu2008 commented 1 year ago

I could implement an option for group-based scaling and if you are interested in getting the llr to 2.0

PengNi commented 1 year ago

Thank you, for now I will use 2.5. If it doesn't take you a long time to implement it, I am very interested. Thank you very much.