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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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methylation calling is not supported for RNA data #162

Closed yao-idol closed 3 months ago

yao-idol commented 3 months ago

Hello,

We recently running f5c-1.4 on RNA004 data. We used the bam files from dorado basecalling. But then we have an error message:

[init_core::ERROR] Methylation calling is not supported for RNA data.

The outputs for "f5c call-methylation" and "f5c meth-frq" are both empty tsv files. (but we do get result from "f5c eventalign".) What is the possible reason for this failure of methylation calling?

Thanks.

hasindu2008 commented 3 months ago

Hello

f5c call-methylation, unfortunately, does not support methylation calling for RNA. Methylation calling is available only for DNA.

Regards

hasindu2008 commented 3 months ago

To add further, The reason is the lack of a trained methylated model for RNA. We do not have any control samples to train a methylated model for RNA. Eventalign works for both DNA and RNA because we have trained nucleotide models for those. Hope I was clear. If not let me know so I can further explain.