I am using Hisat2 to align RNAseq data. I downloaded Rn6 genome from the official web site of Hisat2. It is available on the right side. However, the package does not have gtf file. How I can process the command of $ stringtie -p 8 -G chrX_data/genes/chrX.gtf -o
ERR188044_chrX.gtf –l ERR188044 ERR188044_chrX.bam ?
edit: I did not check the Rattus norvegicus index file, but I believe HISAT2 uses the Rattus_norvegicus.Rnor_6.0.90.gtf.gz to build the index. Check the script they used to build the index, it is bundled together in the same .gz.