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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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RNA004 9-mer model #160

Closed zhongzhd closed 5 months ago

zhongzhd commented 6 months ago

Hello, First of all, thank you for creating f5c and for continuously updating it. I understand that f5c-v.1.4 includes an RNA004 9-mer model. Could you explain the difference between this and a 5-mer model? Thank you.

hasindu2008 commented 6 months ago

Hello @zhongzhd

Why I included a RNA004 9-mer model as default in 1.4 is due to two reasons

  1. the 9-mer model was giving slightly better alignment results (I cannot remember the exact metrics off top my head, can dig my logs and give you if you would like)
  2. to keep consistent with the k-mer size which ONT official k-mer models use at https://github.com/nanoporetech/kmer_models
hasindu2008 commented 5 months ago

Closing this issue for now. If you have any more questions, feel free to reopen.