Problem with Cuffdiff

[honey]

I used Tophat> Cufflink>Cuffcomare>Cuffdiff two comare two samples (treated and control, no replicate) for RNAseq analysis to study differential expression. The output files of CuffDiff does not give any output- just of row of title for promoter Diff., CDS, splicing diff, FRKM TSS group CDS FRKM. The data in the output is only for gene expression.
How is that possible? Am I doing something wrong or it is the way the output will be?
Any suggestion.

Thanks.

[RockChalkJayhawk]

I used Tophat> Cufflink>Cuffcomare>Cuffdiff two comare two samples (treated and control, no replicate) for RNAseq analysis to study differential expression. The output files of CuffDiff does not give any output- just of row of title for promoter Diff., CDS, splicing diff, FRKM TSS group CDS FRKM. The data in the output is only for gene expression.
How is that possible? Am I doing something wrong or it is the way the output will be?
Any suggestion.

Thanks.

There is something wrong with your GTF File.

[honey]

I have downloaded GTF file but everytime I have the same in gene expression it will nor pick up Ensembl Ids too. Is there a know URL which has been used in RNA seq analysis. I am using Hg18
Thanks

[honey]

Well, I sent emails to authors of Cufflink--Cuffdidiff and Topahat but never got any response. I did figured out to map the Cuffdiff IDs to Refflat Hg18 file but now I am stuck with mapping transcripts promoters etc. Unless it has to be done with genomic positions. I believe there may be a simple way to do the same either make Cuffdiff/Cufflinker to talk with Ensembl GTF or else. Any Suggestion Please.
Thanks