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:


Aleks Schein