Direct RNA-seq Nanopore

Question

[frarodmar17]

I want to perform directed RNA-seq Nanopore-derived data and I was not sure if I should use dorado simplex basecaller and then minimap2 to align reads to reference transcriptome or use besacaller aligner function directly. Should I have to take more aspects into account in order to establish a specific data analysis pipeline?

[GenoMax]

I want to perform directed RNA-seq Nanopore-derived data

Can you confirm that you are looking to do direct RNA sequencing that is "adaptive" i.e. for only certain genes you are interested in?

Adaptive sequencing can be tricky with nanopore and the last I knew, direct RNA was not being used for this method.

use besacaller aligner function directly

dorado uses minimap2 under the covers to do the alignments so either way should be fine. You will need to make sure the presets dorado uses match the ones you do.