Hello, thanks to the great resource of this forum I was able to blastn a .fa file against a local blast database. The issue I am having is that the pipeline is blasting against every available sequence in the database. Even with the option: "-qcov_hsp_perc 0.95" I am getting good coverage but species like bacteria and birds are still be queried against.
Going through the ncbi genome site I see that species are broken down into "Kingdom: Eukaryota; Subgroup: Fishes", this in mind I would like to limit my queries to only a specific subgroup or subgroups and not the entire database.
I did not see anything like this in the blastn options yet I am sure there is a way to limit the number of groups a file is blasted against.
Please let me know your ideas so I can give them a try.