I am attempting to use the gffread to convert my GTF to either a GFF or another GTF using the command:
gffread -E CroVir_rnd1.all.maker.final.homologIDs.updatedNov2019_with_myos_geneidmod_edited_with_BPP.gtf -o Crotalus_viridis_annotation_with_BPP_and_myotoxin_2024.12.18.gff
I am not interested in the conversion itself, I am only trying to fix the parent field to my GTF in the attributes column so I can use the Liftoff (https://github.com/agshumate/Liftoff) packages. Using the above command works fine, but it also removes three_prime_utr and five_prime_utr features. I am aware they are not a standard part of the format, but I need them (especially the 3' UTR) as I am doing stuff with microRNAs.