Hello,<br><br>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<br><br>I was fine until running TopHat output, I am having problems with cufflinks and cuffdiff output.<br>
<br>I ran the cufflinks and cuffdiff twice, once with reference annotation and once without reference annotation (Imported form UCSC). <br>Output with reference annotation produced output with gene ids naming usc## <br>Output without reference annotation produced output with gene ids naming CUFF1.###<br>
<br>Can anyone suggest how to get gene names instead of just numbers?<br><br>Thanks<br><br>suz<br>