How to compare CDS gff with genome guided assembled gff

[bioinfonext]

I am working on plant species transcriptome. Its draft genome is known. We want to identify some new transcripts in genome-guided assembly.

I need your help to remove overlapping sequencing by comparing already reported CDS gff file with assembled transcript gff file using StringTie.

Can we also remove the redundancy of transcript which mapping to the same location on the genome by using gff file.

Thanks