Hi! I'm trying to extract exon and splice site information from the gff file (which I downloaded from NCBI: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000214255.1_Bter_1.0/GCF_000214255.1_Bter_1.0_genomic.gff.gz) using the python scripts provided in HISAT2 package extract_splice_sites.py and extract_exons.py) for downstream analysis starting with HISAT2.
The scripts work fine for the example gtf file which I downloaded as supplementary file from the Nature Protocols article ( http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.html ) but when I use these on the gff file the scripts run without returning any error but the output files are empty.
I guess it is because of the gtf fromat (although I see that the information which should be extracted from the gtf file is present in the same columns also in my gff file so I thought the scripts might work as well on the gff file). I simply tried to rename the *.gff to *. gtf, but the python scripts outputed again empty files.
I'll be thankfull for any suggestions on how to extract the exon and splice site information from the gff file!