I have quantified the RNA-seq samples by Salmon. 2 groups are wild-type and 4 groups are Dnmt2 knocked-out. I've put all in one dataset for DE analysis. box plot of their normalized counts shows the median of knocked-out samples are zero, and maximum of 20 reads are assigned to each transcript. now to perform DE by DESeq2 I have 2 questions: 1- whether zero values should be deleted before? 2- to do DE what minimum of counts has to be selected?
thanks in advance