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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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No GpC methylation calling? #141

Closed yangxin-9 closed 1 year ago

yangxin-9 commented 1 year ago

Dear developer, I was wondering that f5c does have a model for GpC methylation calling?

Best, yang

hasindu2008 commented 1 year ago

Is it for r9.4.1 chemistry or latest r10.4.1 you are interested in?

yangxin-9 commented 1 year ago

Thanks for the reply. Nanopolish have a model for GpC methylation calling, but it does not support R10.4 flowcells, So I wonder if the f5c have the GpC model to supports R10.4.1.

hasindu2008 commented 1 year ago

f5c currently does not have a model for GpC for R10.4.1. The CpG model was trained by us using the method described in https://hasindu2008.github.io/f5c/docs/r10train. The control dataset we sequenced for this training was https://zymoresearch.eu/products/human-methylated-non-methylated-wga-dna-set-dna-w-primers, and it only has CG sites methylated. If there is a suitable control sample like this for GC that you are aware of, we could try to train a model, as the method would be exactly the same.

yangxin-9 commented 1 year ago

Thank you for the answer. I don't have a suitable control sample yet.

best wishes, yangxin