Accidental mapping of eukaryotic reads in a metagenomic dataset 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?
If you know the eukaryotic contaminant present you could use bbsplit.sh from BBMap suite to split/bin reads first using a reference for that contaminant (into one or as many bins as reference sequences you provide).