Hello Giuseppe,

If you haven't resolved this yet, then I would suggested double checking that the chromosome identifiers in the reference annotation file are exactly the same as in the reference genome. You can run Picard's tools to get summary stats on Tophat's BAM outout files to see the reference genome idenifiers, or use SAMTools' BAM->SAM to examine.

In general, it is simpler to change the reference annotation's identifiers to match those in reference genome. As the file is small, a simple find/replace in a text editor is a common solution.

Hope this helps,

Jen
Galaxy team

On 9/10/13 3:22 PM, Ianiri, Giuseppe wrote:

Hy guys,
I am performing some RNA sequencing. I am using a gtf file as a reference annotation for the cufflink - cuffmerge steps. Then when I do the cuffdiff I find something strange. Where there is the gene name, the corresponding values (all of them!) are 0, where there is no gene name there are values of expression, fold change etc.

Does anyone have an idea of what is going on? I haven't find any similar question in the Galaxy archive.

Also, I tried to visualize my outputs (TopHat Cufflink Cuffmerge) using Trackster but it gives me an error. Is anyone experiencing the same problem?

Thanks,

Giuseppe
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