Intron retension calculation (non-model organism)?

Question

[Shero]

I'm trying to calculate the intron retension difference between 2 conditions in nonmodel organism which is not well annotated as its GTF file only contain exons not introns. As beginner in bioinformatics I tried to use IRfinder and iRead but didn't work with me. Any useful suggestions?

[husensofteng]

as it was mentioned, GTF files usually don't contain introns. I have written a gtf_plus_intron python script to add introns to a GTF file:

python gtf_plus_intron.py -i input.gtf -o output.gtf