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
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.cufflinks@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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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