I have used Hisat2 to map some RNAseq reads against a brand-new genome assembly from the same species. In the literature the same reads were mapped against the reference genome of a different species of the same genus (because, despite the differences, this reference genome is more complete and better annotated). As expected, the alignment rates were around 10-15% higher when mapped to the same species. However, since this genome is brand new there is no annotation available yet, so I used StringTie to make myself a basic annotation for gene count and Differential Expression Analysis.
Is there any way to know which gene ids between both reference and self-made annotations match to the same RNA reads, and then identify gene ids that are present in one but not the other?