I am working on the genome analysis of Rousettus_aegyptiacus organisms from data obtained ENA database. After the quality checking (Fastqc) of the reads, I have done alignment with hiasat2, index building carried out using the file from NCBI: ftp.ncbi.nih.gov/genomes/Rousettus_aegyptiacus/CHR_Un/9407_ref_Raegyp2.0_chrUn.fa.gz. Then I tried to check the overall alignment quality score for a few samples, it ranges 92-93%. Now I want to perform stringTie for assembly, In this step, I need the GTF file. I couldn't find it. Please tell me how do I get or generate GTF fie for this organism.
Your response highly appreciated!