ONT direct RNA with Tombo and MINES

[akk01]

while processing the data with Tombo before using MINES, which reference fasta should be used for ONT direct RNA sequencing data - genome or cDNA fasta.

[yefei521]

In Tombo [https://nanoporetech.github.io/tombo/modified_base_detection.html], It said that you should provide transcripts as reference when processing Nanopore DRS data (call m6A).
About how to extract transcripts, TBtools may be help a lot for you. (exon + downstream + upstream)