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I have 3 groups for the RNA-seq analysis (Control, treatment A and treatment B). There are 2 replicates for control and treatment A and 3 replicates for treatment B (lost 2 replicates due to a mistake in sample handling). May I ask how will the inconsistent replicate numbers impact the results (e.g. DEGs)?

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It will not do any harm other than a reduction in statistical power compared to more samples per group. Common analysis tools such as DESeq2, edgeR and limma will work on unequal sample size just fine.

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