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 

I look forward to the update, will that mean another version of Cuffdiff again?

Kind regards,

From: Jeremy Goecks []
Sent: Thursday, August 22, 2013 8:04 PM
To: Johanna Sandgren
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 

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.


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