After doing what was recommended to me in my previous post ( Match predicted sequences to reference genome to generate data for annotation GTF ), I ended up with two annotation files. EVM produced an annotation on a scaffold level ("scaffold1234"), BLAT produced an annotation on the contig level ("RDRX12302"). Now I am wondering how do I merge the information of these two GTF files? I do know which contig is part of which scaffold (the reference genome lists them as: ">RDRX12302 isolate A scaffold1234, whole genome shotgun sequence", but I imagine that the position numbers put out by BLAT are sensitive to contig identity and cannot just copied over to the respective scaffold names.
I would be grateful if you could point me into the correct direction.
Thank you! Joe