Hello everyone,

This is an RNAseq assay, for a apomictic plant and 12 clones of each genotype 30 millons reads for each library

I have a very simple experimental design for screening differentially expressed genes on drought.

2 contrasting genotypes, 2 contrasting situations and three different times.

For the control libraries I have biological replicates, and for the stresses just technical replicates. My question is how to deal with this difference?

I can use the Bio rep to assert there is difference between groups and no difference inside groups and use this assessment for all the groups and then pool the Tec rep for the analyses?

Or there is a better idea how to proceed?

Thank's in advanced.