I am trying to use Geneious to do some expression analysis using Dseq2. I was going through the tutorial and the reference sequence they used was super complete (NC_006841). It was annotated and it had the name of the proteins, min, max, length, and direction. I'm just wondering where they even got that reference sequence from? The best I can get is just a fasta file with the genome. I'm working with Drosophila so I was guessing there is a reference sequencing out similar to the one they used in their tutorial.
I can't help you with Geneious, as I don't use it - so far, I haven't even been able to pronounce its name, so I pretend it don't exist. There are several detailed workflows and tutorials out there (one example, among many, here), but generally speaking, you have to:
1) map your sequencing reads to a reference genome or transcriptome
2) summarize read counts using an annotation
3) perform differential expression analysis
Flybase has a very complete D. melanogaster genome and annotation, but it should be the same or very close to those from Ensembl or NCBI.