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Question: Differentiating between Replicates and Conditions - Cuffdiff
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gravatar for tom_denyer
12 months ago by
tom_denyer • 0
tom_denyer • 0 wrote:

Hello

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!

Thanks

Tom
rna-seq conditions replicates cufflinks cuffdiff • 551 views
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modified 12 months ago by Jennifer Hillman Jackson ♦ 25k • written 12 months ago by tom_denyer • 0
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gravatar for Jennifer Hillman Jackson
12 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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: https://galaxyproject.org/learn/

Thanks, Jen, Galaxy team
ADD COMMENT • link written 12 months ago by Jennifer Hillman Jackson ♦ 25k
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