I think this is an old but common problem that many people encountered when running the cufflinks with the ENsemble annotation references.
I have modified the annotation file download from Ensembl (GRCh37.V75). When I selected the option -G (use reference annotation), the cufflinks could successfully ran. However, when I selected the option -g (use reference annotation as guide), the cufflinks running was failed, showing the duplicate GFF ID error. Does anybody have the same problems, or you may give me some suggestions.explanations on such problems.
I used the canonical genome reference GRCh37_Ensemble_75 (without unplaced contigs).