Question: Does 'differential' = 'unique' = 'specific' in Galaxy?
gravatar for dandrew
3.4 years ago by
United States
dandrew10 wrote:



I've done about a dozen RNA-seq datasets and the results i get as "differential' are either a few seqs uniquely expressed in only one of the treatments or an empty set. I get hundreds of transcripts expressed at varying levels between the two treatments but these are never called as being significant by Galaxy.

Philosophically, I don't see how this could be. I'm interested in more than on/off changes. What is the point in doing time course experiments if you can't statistically watch differential expression rise and fall. 

So, what do i need to change in my analysis in Galaxy to see significant (+/-) 2-fold differences? Is Galaxy designed to only recognize specificities?

Can someone send me a link to a history that has statistically significant, 2-fold (or greater) non-unique differences or, explain how this is done with Galaxy?



rna-seq galaxy • 718 views
ADD COMMENTlink modified 3.4 years ago by Jennifer Hillman Jackson25k • written 3.4 years ago by dandrew10
gravatar for Jennifer Hillman Jackson
3.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


It may help to review the publication for the protocols and the associated web documentation to determine optimal parameters for your experiment. Note that some tools (such as Cummerbund) in the tutorials below are available from the Tool Shed for use in a local or cloud Galaxy (are not on

Tuxedo pipeline resources (for StringTie, see the link at the bottom of the tool form):

Best, Jen, Galaxy team

ADD COMMENTlink written 3.4 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 173 users visited in the last hour