Hello Aleks,

Chromosome names must be exact between all input files). Also, the SAM file and GTF file both must be sorted the same way. This FAQ may be of interest:
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq

If still a problem, please share the history with me directly either using my email address or generate the share link and email to me (only). Use "Options -> Share or Publish", not just your sessions browser URL.

Best,

Jen
Galaxy team

On 7/22/11 8:45 AM, Aleks Schein wrote:

Dear all,
I am trying to run Cufflinks installation in Galaxy on Solexa RNAseq
samples from HeLa cells.
Running Cuffcompare, according to the manual, should produce a tmap
file, listing FMI values for detected isoforms. However, my files only
have either "100" or "0" in FMI field. And FPKM column contains only zeros.
Is there something wrong with my input files, or parameter settings? Or
is it rather a specific issue with Galaxy Cufflink's installation?

The data in question is available here:
http://main.g2.bx.psu.edu/u/aleks/h/guided-assemblyadvanced

Thanks,

Aleks Schein



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