Question: Differentiating between Replicates and Conditions - Cuffdiff
gravatar for tom_denyer
12 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 12 months ago by Jennifer Hillman Jackson25k • written 12 months ago by tom_denyer0
gravatar for Jennifer Hillman Jackson
12 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 12 months ago by Jennifer Hillman Jackson25k
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