I am trying to do the differential expression analysis on my long-read nanopore data. I used nanopore recommended workflow to align the reads (it's called wf-alignment: https://github.com/epi2me-labs/wf-alignment). I want to use the output from this workflow to do DESeq2 analysis, but I am lost how I can bridge the two workflows! I get all of these files from running the alignment workflow:
I am a wet-lab person and pretty new to bioinformatics world, so please include all the basic stuff I may ignore naively! Appreciate your help!