Re: [galaxy-user] Cuffdiff changes

[Jeremy Goecks]

 Where can I see which version are being used?

You can see both the Galaxy tool version and the Cuffdiff tool version (when 
available) by clicking on the 'view details' icon (the 'i' at the bottom of an 
expanded dataset). Right now the Cuffdiff version is not displayed, but that 
will change when our server is updated.

 What does Cuffdiff(version 0.0.5) mean then?

That is the version of the Galaxy wrapper; the wrapper provides the interface 
between Cuffdiff and Galaxy.

 What version was it before?

I think Cuffdiff version was 1.3.1 previously.
 
 I look forward to the update, will that mean another version of Cuffdiff 
 again?

The wrapper will be updated but not Cuffdiff itself.

J.

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Re: [galaxy-user] Cuffdiff changes

[Johanna Sandgren]

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.goe...@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.

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