Dear all, I have found this paper: piRNAs Are Associated with Diverse Transgenerational Effects on Gene and Transposon Expression in a Hybrid Dysgenic Syndrome of D . virilis
in which there is this statement: "We did not perform DESeq2 analysis because estimation of the dispersion parameter with DEseq2 is unlikely to be robust with about 200 TEs, compared to standard mRNA-seq analysis that estimates the dispersion parameter using thousands of genes".
How many genes is advisable to use with DESeq2?
Thank you.
Riccardo