How to compare CDS gff with genome guided assembled gff

Question

[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

[shenwei356]

I'm not familiar with RNAseq analysis. But according to your description, bedtools2 and bedops may help. gff can be converted to bed by gff2bed from bedops.