How to evaluate RNA-seq quality if having three replicates?
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5.9 years ago
biolab ★ 1.3k

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 • 2.1k views
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5.9 years ago
poisonAlien ★ 3.0k

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.

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Hi, poisonAlien,

Your answer is very helpful. Thank you very much!

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