Hello Irene,

This issue is similar to the original. The input GTF for this run (dataset #15) has tss_id populated, but not p_id. The p_id attribute is required for the CDS calculations.

http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff_input

   (quote) Cuffdiff Input:

   Attribute    Description
   p_id         The ID of the coding sequence this
   transcript contains. This attribute is attached by Cuffcompare
   to the .combined.gtf records only when it is run with a reference
   annotation that include CDS records. Further, differential CDS
   analysis is only performed when all isoforms of a gene have p_id
   attributes, because neither Cufflinks nor Cuffcompare attempt to
   assign an open reading frame to transcripts.

Dataset #15 was created from a CuffMerge run (which runs Cuffcompare as a component). Examining the selections used (clicking on the blue arrow "rerun" icon), shows that the option "Use Sequence Data:" was set to "No". Changing this to "Yes" and using "Choose the source for the reference list:" as "Locally cached" (and double checking that all inputs are assigned to hg19) will assign p_id. Note that this will be true only for those transcripts that are associated with reference annotation transcripts containing coding regions (in your data: 'nearest_ref "NM_XXXXX"', not "NR_XXXXX". NR_ human RefSeq transcripts are non-coding).

   Galaxy's CuffMerge tool form has this option labeled:

   (quote) Use Sequence Data:
   Use sequence data for some optional classification
   functions, including the addition of the p_id attribute
   required by Cuffdiff.


Thanks!

Jen
Galaxy team

On 7/21/12 11:04 PM, i b wrote:
Hi,
I ran again cuffdiff using the cuffmerge as gtf.
The following dataset were empty:

128: Cuffdiff on data 12, data 14, and others: CDS FPKM tracking

  127: Cuffdiff on data 12, data 14, and others: CDS FPKM differential
expression testing

126: Cuffdiff on data 12, data 14, and others: CDS overloading
diffential expression testing

The others have data downloadable as excel.

any explanation???????

Thanks,
ib

On Fri, Jul 20, 2012 at 12:10 AM, Jennifer Jackson <j...@bx.psu.edu> wrote:
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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--
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http://galaxyproject.org

--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
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