This is a question from /u/wipeyourmit on reddit. The original post can be found here.
If I have a metagenomic dataset that contains reads from both eukaryotes and prokaryotes and then I annotate by running DIAMOND or HMMER against a bacterial database how much of a risk do I run of eukaryotic reads being annotated in the process?
I was hoping to use the eggNOG mapper to search against the bacterial and archaeal databases and to exclude the eukaryotic portion of my dataset. Is the eukaryotic filtering something that I would need to do in a step prior to this?