I have an RNA-seq dataset and I am using
DEseq2 to find differentially expressed genes between the two groups. I used pre-filtering to remove any genes that have no counts or only one count across the samples.
furthermore, I want to:
remove genes in low counts by using a base mean threshold.
remove genes that have low counts compared to the rest of the genes.
Is there a common threshold used for the baseMean or a way to work out what this threshold should be?