I ran Tuxedo at Galaxy (public, online), using TopHat2-Cufflinks-Cuffmerge-Cuffdiff. I expected my Cuffdiff output to contain gene_name, so that I could directly identify genes in downstream analyses. However, it seems to be missing and I only have a list of transcript ids (all isoforms) for each gene instead.
I used Reference genome at all steps (Cufflinks, Cuffdiff) downloaded from UCSC with Ensembl annotations. Now when I e.g. open a file with gene fpkm tracking, my columns tracking_id and gene_id are the same and contain XLOC ids. The column with gene_short_name contains a list of Ensembl transcript ids (although it's a gene file, it just puts all transcript ids belonging to that gene there).
So to me it looks like the columns are not filled appropriately. I wondered if somebody knows what I might have done wrong or has encountered a similar problem.
Below a fragment of a file - the gene_short_name column contains ENST ids in other files which i checked too. This is a gene fpkm tracking file...
Any ideas on what might've gone wrong are very much welcome!