First of all, can you tell me how necessary it is to generate read counts in an RNA-Seq differential expression analysis and what it is for? I’m working with the reference genome of Arabidopsis thaliana and paired-end data.
I checked the tools FeatureCounts and HTseq counts and both of them require a GTF file, but the Arabidopsis genome is not listed there, should I do my own GTF file with the whole genome or just with some genes?