Hello Michael, I ran DESeq2 to get DEGs between case and control groups. I know that DESeq2 filters lowly expressed genes. So is it possible to get highly expresssed genes in each group? I do not want to set an arbitrary threshold, such as FPKM>1, to define higly expressed genes. I want to get the highly expressed genes from DESeq2 results. Thanks

We don't have a definition in DESeq2 of "highly expressed". Our filters are solely for practical purposes of detection, not for determining when a gene is expressed or not.