I performed de novo transcriptome assembly. Have the FASTA file that I am using as my reference and also performed alignments of my reads back to that. I have been using stringtie to create gtf files for the differential expression analysis (counting requires a gtf file) but I am trying to do this at gene level. Stringtie creates its own IDs for alternative splicing/isoforms. I do not want this. I can't see a way around this so is there a way I can create a gtf annotation file based on my fasta file I use for my reference?