DESeq analysis with different replication

Question

[maxgen]

Hello-

I am running RNASeq analysis by using Kallisto and DESeq pipeline. Is there a way to compare two different replications in DESeq (or any other statistical package). eg: 4 replications of WT and 3 replications of KO.

Thank you!

[piyushjo]

Minimum replicate requirement is 2. You can have unbalanced dataset. DESeq2 also sends a warning that minimum replicate required is 7, but I have still done lower replicates for one of the condition.

Answer 1

[ATpoint]

Differences in replicate numbers are not a problem unless the differences is very big. Your numbers are perfectly fine. Simply follow the DESeq2 vignette for differential analysis.

Answer 2

[maxgen]

Thank you! These comments are really helpful. I did run DESeq, PCA and Volcano plots seems to be okay.