[galaxy-dev] cuffdiff output

Hello, I am new to using Galaxy tools. I am running paired end RNA-Seq data on Galaxy and I want to differential gene expression between control and treated samples I was fine until running TopHat output, I am having problems with cufflinks and cuffdiff output. I ran the cufflinks and cuffdiff twice, once with reference annotation and once without reference annotation (Imported form UCSC). Output with reference annotation produced output with gene ids naming usc## Output without reference annotation produced output with gene ids naming CUFF1.### Can anyone suggest how to get gene names instead of just numbers? Thanks suz