I'm doing the single cell RNA-Seq and trying to find out genes showing different expression under two treatments. Thus my first step is to put two datasets from different treatments together and the second is to compare the difference.
When I merge two single cell RNA-seq datasets together, I notice that there are some unique genes from the previous two datasets and they are maintained by Seurat::merge(). I'm wondering whether I should keep these unique genes? Will they affect the downstream analysis of differential analysis?
Thank you in advance!