Hi, I would like to do differential expression analysis of RNA-seq data between 2 conditions, and I only have 2-3 samples per condition. Do you recommend me to use DESeq2 method for this case, or which one? Would results be reliable? I had more samples but I had to removed them from my analysis because of poor quality.
Depends on what the samples are. You can still run them through DESeq2, you have biological replicates, it just may be underpowered depending on what you're looking for.
DESeq2 is good for gene level analysis. Salmon/Kallisto + Sleuth for transcripts.
I have published papers where we only had 3 replicates per condition in a control / condition setting. As long as you have more than 2 replicates, technically you can use DESeq2 for differential analysis and meanwhile you may discuss the lack of replicate in your paper if you feel it worth to mention anything about it.