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,