I'm new to bioinformatics, I have a question which may seem easy. For my RNA-seq analyses, I was using HISAT2 with already-indexed reference genome downloaded from HISAT2 website for Homo sapiens. And as GTF I was using the one I downloaded from Ensembl. After some runs, I thought this usage might be wrong, because I downloaded reference genome and GTF from different sources (HISAT2 website does not have GTF) and they might not be matched. So I've decided to download a new reference genome from Ensembl and index it myself, and using the corresponding GTF file from Ensembl with the right version number (v93). Is there any incompatibility between my previous GTF
Homo_sapiens.GRCh38.92.gtf and reference genome? How should I use them?