I am working with cufflinks,cuffdiff for RNA-SEQ data.
In cufflinks, If we are not looking for novel isoforms, we need to use GTF file with cufflinks ( -G GTF ).
My question is that if we do not want any novel isoforms, we can skip the cufflinks step in Tuxedo protocol. We can use TopHat and cuffdiff to get differential isoforms. But in that case why cufflinks has an option for -G GTF.