How to evaluate RNA-seq quality if having three replicates?

Question

[biolab]

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 definitely 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 available to statistically assess RNA-seq quality? THANK YOU very much!

Answer 1

[poisonAlien]

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.

[biolab]

Hi, poisonAlien,

Your answer is very helpful. Thank you very much!