Hi there,

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:

merged.mapula.json

merged.sorted.aligned.bam

merged.sorted.aligned.bam.bai

combined.fasta

combined.fasta.fai

final_merged.csv

jbrowse.json

params.json

wf-alignment-report.html

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!

What you need now are gene counts. Given that bam file, I think your best bet is FeatureCounts from the subread suite of programs. You of course also need a gtf which has the coordinates of your genes and exons.

(Why not use wf-transcriptomes?)