How to do differential expression without having replicates

Question

[minoo]

I have two controls and one treatment sample. I cant use Deseq2 as there are no enough replicates. What is the best way to find differential gene expressions?

Answer 1

[ATpoint]

You can use DESeq2 with 2 vs 1 with no problem as you habe replication in one group, so all estimated parameters are based on this. Obviously underpowered but it will work with the tool.

Answer 2

[Nicolas Rosewick]

question asked 1000 times here : Rna-Seq Biological Replicates...

Quick answer : you can't . Try to have biological replicates otherwise you will never have confident results.

[dsull]

If you have two replicates in one group but no replicates in another group, you should be able to proceed as normal with DE analysis. It seems like the original poster had replicates in their control group.