I see more and more papers these days that use a read cut off before deseq2 analysis, I wonder what is the rational and/or how do they arrive at how many reads is a right number..for example from one of the papers
DESeq2 was applied to genes having more than 20 reads in half the number of samples
^ this study had n=8 4wt and 4ko.
i could not comprehend how did they arrive at the number 20, even if they did what if the differences are genotype driven
more over DESeq2 has independent filtering which takes care of low counts no?
Is there a way one can plot counts and determine what is a right threshold for pre filtering