Hello Irene,

Yes, this is can be the result if your source GTF data did not have the full compliment of attributes needed by Cuffdiff to perform these calculations.

The primary tool documentation covers this information here: http://cufflinks.cbcb.umd.edu/manual.html#fpkm_track

The iGenomes datasets are a popular choice for this reason. A version of UCSC RefGenes is available for certain genomes. Please see: http://cufflinks.cbcb.umd.edu/igenomes.html (scroll down on page in some browsers to find table)

Galaxy has one of these already loaded, mm9 genes.gtf, in the "Shared Data -> Shared Libraries" section on the public Main server. More iGenomes .gtf files will likely be added here, sometime after the GCC2012 conference. For now, locally download to your own system/desktop, uncompress, and just load the GTF file to Galaxy.
Consider FTP for larger datasets: http://wiki.g2.bx.psu.edu/FTPUpload)

More resources include the author supported help email at tophat.cuffli...@gmail.com and seqanswers.com (where the authors often post).

Hopefully this helps,

Jen
Galaxy team

On 7/19/12 1:38 PM, i b wrote:
Hi,
I ran cuffdiff using Refseq genes as GTF and two groups of BAM. Group
one has two replicates (treated) and group two only one replicate
(untreated).

When looking at the outputs the following are empty (1 line):

TSS group FPKM tracking
TSS groups differential expression testing
CDS FPKM tracking
CDS FPKM differential expression testing
CDS overloading diffential expression testing
promoters differential expression testing
splicing differential expression testing

the other four outputs have data downloadable as excel.

Is this normal?

thanks,
ib
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