Deseq2 analysis output too many DEGs

Hello everyone.

I have two samples, WT and Mutant. I performed Featurecounts, obtained the count file, remove reads bellow 20 counts and perform the deseq2 analysis. However, even filtering pvalue<0.001 and a fold change of 2, I still have 19 000 DEGs. I am working with Nicotiana tabacum. Any idea why?

Hi @brebelo

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