search

jts / nanopolish

Signal-level algorithms for MinION data
MIT License
568 stars 159 forks source link

Do I need to convert U to T for nanopore direct RNA m6A analysis #1115

Open wuy24 opened 1 year ago

wuy24 commented 1 year ago

Hi,

I am analyzing m6A call from nanopore direct RNA sequenceing data. After basecalling, the direct RNA reads contain U instead of T. I wonder if it is necessary to conver U to T in fastq file in order to do m6A calling. And if I converted U to T in the analysis, will it affect the results? Thank you!

Best, Ying

jts commented 1 year ago

Hi @wuy24,

Nanopolish itself doesn't call m6A so I would consult with the package you are using for m6A identification. But in general yes, Us should be converted to Ts for nanopolish.

Jared

wuy24 commented 1 year ago

Hi Jared,

Thank you very much for your quick reply! Yes, I am using m6anet for m6A call and it require the eventalign.txt from nanopolish eventalign. I will probably convert U to Ts to run nanopolish and consult with the package. Thank you!

Best, Ying