I have combined two gff files for my annotation. One GFF represents chromosomes 1-29 + X and second GFF represents Y chromosome. The same situation is with genome (I have combined two genomes for my purposes).
The problem is with ID and Parent field in GFF because they are overlapping. I mean Y chromosome has the same ID as 29 chromosome:
Y Gnomon gene 2502499 2571410 . + . ID=gene32386;Dbxref=GeneID:100849399;Name=LOC100849399;gbkey=Gene;gene=LOC100849399;gene_biotype=protein_coding
and the same ID (gene32386) here:
29 Gnomon pseudogene 37912602 37922321 . - . ID=gene32386;Dbxref=GeneID:615840;Name=LOC615840;gbkey=Gene;gene=LOC615840;gene_biotype=pseudogene;pseudo=true
How can I fix that problem? Because of that situation I cannot do annotation of my Y chromosome. Should I modify ID and Parent field in my GFF or what?