I was trying to extract splices sites of my -gtf file but I had no success with neither "hisat2_splice_sites.py" nor "awk" command. For both options I just had a blank file as output. My final goal is use the splice sites forhisat2-build --ss --exon. For some reason, I could do that with human gtf files but HIV. I tried to download several files of many data site such as NCBI, UCSC genome Browser, Esembl and ENA. Someone could help with another data site for retrieve gff/gtf files, or even how to make a new one by myself? OBs: I downloaded gff files and then converted with gffread command
Thank you guys in advance!