I am trying to analyze RNA-seq fastq files by using Trimmomatric → FastQC → Hisat2 → Cufflinks. I am uploading my reference genome as well as the GTF file but the output files do not include the annotated genes, the genes are labeled “CUFF.5, CUFF.21” instead. I tried modifying the GTF file but it still won’t work. I can not find an example of the proper GTF file format to be able to know if I need to edit any columns or where it is pulling this information from. Trying to get read count per gene and also ranked list of the most abundant genes. Eventually to also do differential expression gene analysis.