[galaxy-user] cuffcompare inputs

Dear all, given 3 samples, 1 control and 2 treated replicates when I do cuffcompare to produce the gtf input for cuffdiff, do I have to run it with or without the cufflink control? E.g. Cuffcompare with only my 2 treated replicates?--------------use this gtf to run cuffdiff Cuffcompare 1 contro and 2 treated replicates?--------------use this gtf to run cuffdff Thanks a lot ib