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GoekeLab / m6anet

Detection of m6A from direct RNA-Seq data
https://m6anet.readthedocs.io/
MIT License
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reference genome or transcriptome #30

Closed sdwien closed 2 years ago

sdwien commented 2 years ago

Dear m6anet Team,

I am using m6anet for the first time with mouse data from ONT directRNA sequencing. I preprocessed the reads with guppy (basecalling), minimap2 (alignment to the reference genome and to the reference transcriptome, from Gencode) and nanopolish as described in #9 . However, I would like to make sure about the reference: Do you usually use the reference genome, or a reference transcriptome (one sequence = one transcript)? Many thanks for your help. Best regards, Sophia

chrishendra93 commented 2 years ago

Hi @sdwien , glad to hear that you want to try out m6anet for this! We usually use reference transcriptome for this, make sure you include --signal-index when running nanopolish eventalign as described in the issue you referred to. Let us know if it works for you!

Christopher

sdwien commented 2 years ago

Thanks, that's all I needed to know. Running it now... Best, Sophia