Hi I am currently working on my experimental design and would like to use DESeq2 to analyze my data. 

For this experiment I would like to understand the differences among genotypes under a treatment.  I have 5 genotypes and would like your advice on the minimum number of biological replicates. Can I get away with 2 biological replicates per genotype per treatment?

Thanks for your time,

Catalina

It depends strongly on the effect size, sequencing depth, and biological variability. 

You can plug these values into a power calculator for RNA-seq, to see if n=2 per group will be reasonably powered:

https://bioconductor.org/packages/release/bioc/html/RNASeqPower.html

https://www.bioconductor.org/packages/release/bioc/html/PROPER.html

In order to come up with typical effect sizes, sequencing depth and estimates of biological variability (dispersion), you can have a bioinformatician or biostatistician analyze a similar dataset (e.g. same organism, similar treatments).