Thanks for quick reply. Where can I see which version are being used? It does not say in the attached (in my first e-mail) info-view after the run.. What does Cuffdiff (version 0.0.5) mean then? What version was it before? It is a great difference in number of DE genes.. I mostly meant it was the same now in August with more DE genes for all different type of analysis that I have previously done (consistent new results with no settings changed), I really do not see more DE genes when 5 vs 6 samples compared to 1 vs 2 samples. But that might be due to more biological reasons. I look forward to the update, will that mean another version of Cuffdiff again? Kind regards, Johanna From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] Sent: Thursday, August 22, 2013 8:04 PM To: Johanna Sandgren Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Cuffdiff changes I am wondering why Cuffdiff suddenly gives many more significant DE genes? Cuffdiff was recently updated to version 2.1.0; this update likely explains the different results that you see. I have rerun several analysis, also with more samples in each group, all give much more significant genes. Why? More samples = more power to accurately estimate expression levels = more DE genes. Also, will replicate information soon be included in output files? Replicate data will be available when we next update our server. This should occur in about 3 weeks. Best, J.