Hi, I have a question about using lfcshrink() vs results() to identify DEGs.

I'm currently identifying upregulated DEGs as having padj<0.01 and log2FC>1. Using unshrunken results, I am getting around 800 DEGs which is higher then I expected. A lot of these DEGs come from genes with low counts, so if I apply lfcshrink() and use these shrunken log2FC to identify DEGs, I end up with around 400 DEGs.

It seems like lfcshrink() is used for ranking DEGs, can it also be used to identify DEGs? I'm currently filtering low counts by CPM. Is there anything else I can use to clean up my data?

Yes, you can use lfcShrink with svalue=TRUE to identify DEG. See the apeglm vignette for some discussion about s-value compared to q-value (padj).