Question: How to evaluate RNA-seq quality if having three replicates?
gravatar for biolab
5.1 years ago by
biolab1.2k wrote:

Dear all,

Following my post (RNA-seq triple replicates),  I have a further question about evaluation of RNA-seq replicates.  Previously my colleagues faced a situation, in which a reviewer in a journal requested RNA-seq replicates.  I think this is probably true for many of you.  Therefore, RNA-seq replicates are definately necessary. 

I want to ask you how to evaluate RNA-seq quality if having three replicates (I think it is easier for two replicates, as scatter plot is enough).  Are there any tools avaliable to statistically assess RNA-seq quality?  THANK YOU very much!

rna-seq • 1.9k views
ADD COMMENTlink modified 5.1 years ago by poisonAlien2.8k • written 5.1 years ago by biolab1.2k
gravatar for poisonAlien
5.1 years ago by
poisonAlien2.8k wrote:

Check out Section 2.2 of DESEq2 vignette. Sample-to-sample distances and Principal Component Analysis should show clustering of replicates, unless there are any batch effects or different experimental designs.

ADD COMMENTlink written 5.1 years ago by poisonAlien2.8k

Hi, poisonAlien,

Your answer is very helpful. Thank you very much!

ADD REPLYlink modified 5.1 years ago • written 5.1 years ago by biolab1.2k
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