Hi, I made and miRNA seq experiment and I'm analyzing it. I generated a miRNA counting table based on mirbase (v22). The problem is that hundreds of miRNAs had 0 counts in all samples, and I don't know if I should remove them before DESeq2 analysis. In my opinion, those miRNAs should be excluded before analysis, since they can impact in the adjusted p-value (I guess), but I'm not sure what to do. Anybody knows the right way to deal with this type of data and how to analyze them? Thanks

This is covered in the workflow (rnaseqGene).

You can filter them, but no they will not negatively affect the multiple testing because of the way results() works.