recommended threshold for the log likelihood ratio

[PengNi]

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]

Hi

For f5c meth-freq, I have not implemented this scaling based on the group size discussed here jts/nanopolish#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]

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

[hasindu2008]

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

[PengNi]

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.