I currently have two GTFs which are incomplete. What I mean by this?. For example, in one of them I have 5000 genes and in another I have 7000, however, there are 3000 genes that coincide (they are the same). Therefore, I would like to create a GTF with the 5000 + 7000 genes, but without duplicating the 3000 identical genes, so I would have in the end a GTF with 9000 genes (not 12000).
What could I do? I think both Cuffmerge and Cuffcompare are useless in these cases.
All the best