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GoekeLab / m6anet

Detection of m6A from direct RNA-Seq data
https://m6anet.readthedocs.io/
MIT License
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Kmer #24

Closed al3xMlt closed 2 years ago

al3xMlt commented 2 years ago

What are possible reasons, why a DRACH motif is not processed?

Kind regards

Alex

chrishendra93 commented 2 years ago

Apology for the late reply,

It's either they do not have enough reads or when aligned with nanopolish, the reference kmer and model kmer are different in nanopolish eventalign

al3xMlt commented 2 years ago

Do you know what can cause the problem, that aligning with nanopolish the refernce kmer and the model kmer differs? Is it a basecalling error? And If yes, cant this be associated (if EpiNano is to believed) with a m6A modification? Also the publication of João H. C. Campos et.al observed C > U change in the fourth position of DRACH which affects methylation. This positions would also not be processed right? I am very curious about your expertise and your thoughts about it! Best -alex