I feel like this might be a really silly question and I've been going back and forth for awhile and I think confusing myself- so sorry if this is dumb.
I am using Seqmonk to visualize genes in an assembly (but I suspect the issue would be the same in any visualization software). I am trying to identify promoters of specific genes to determine if they are differentially methylated. Genes on the forward strand (highlighted in red), the promoter would inherently be upstream- in this case to the left (i.e. if my start site was 5000 and the end site 6000, I would assume I could find my promoter to the left of the start site between 3000 and 5000 bases.
My confusion is what happens with genes that are on the reverse strand (in blue here). Start site and end site could be the same (5000 and 6000- as end sites are always bigger than the start site). Does this mean that in the software, the promoter is expected to be on the right hand side (i.e. bases 6000-8000)? This has been my going thought but now I wonder if having bases that seem downstream (because they're bigger) makes sense, even though it really does because downstream on the forward strand would be upstream on the reverse strand. Or if I need to always do 3000-5000 bases as the promoter, regardless of the the strand of origin.