I am very new to programming in general, and I'm trying my best to teach myself R for analyzing RNA-seq data we have.
I am using this guide and have gotten to the step where I need to align to mapped reads. however, when I use the GTF file to align my reads, I don't get any alignments.
I suspect that I used the wrong file for the genome alignment, the wrong GTF, or both.
Can someone please confirm or deny?