2.4 Differential gene expression analysis
We used DESeq2 to compute log-fold changes in response to environmental
contrasts (Love et al., 2014). Prior to running DESeq2, we removed genes
with mean read counts less than three to eliminate bias from very low
expressed genes. We encoded the non-stressed and stressed populations
for each contrast as “control” and “treatment” in DESeq2,
respectively. For sequencing runs from Dixon et al., 2014, we ran DESeq2
on all the runs, including the genotyping replicates used for
transplanting in the original study, and added “transplant location”
as an additional variable to our analysis to remove the effect of
transplant location.