cufflinks with GTF file

[goutham.atla]

Hi,

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.

[yueluo]

I think in your case, you can skip cufflinks and use a reference gtf as input for cuffdiff.

I don't have an answer to your other question though.