Question: Differentiating between Replicates and Conditions - Cuffdiff
gravatar for tom_denyer
9 months ago by
tom_denyer0 wrote:


I am new to RNA-Seq analysis and am struggling a bit with setting up the CuffDiff

I have two conditions and for each I have 3 replicates. I want to compare significantly different expression between conditions but also between replicates within conditions.

Can I run this all at once and if so how?

I get the impression that I need to run CuffMerge first to put all 6 datasets together into one file but after running this with the two conditions (containing 6 datasets each), there seems to be no distinction between replicates.

Should I run the 6 'assembled transcripts' files from Cufflinks separately against all three replicates of each condition? That seems to lead to many files.

Hope that makes sense!



ADD COMMENTlink modified 9 months ago by Jennifer Hillman Jackson25k • written 9 months ago by tom_denyer0
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Try the Cuffdiff option to "Include Read Group Datasets" with Cuffdiff. This might produce the data you need the most.

Another alternative for DE is to use a count-based tool like Deseq2.

Please see the RNA-seq tutorials here for example workflows:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 9 months ago by Jennifer Hillman Jackson25k
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