I have an assembled transcriptome from an organism hosting various symbionts and I'm now interested in how many of my contigs hitting to the different kingdoms. What I've found so far is the -window_masker_taxid that filters my dataset based upon what kind of taxis I put there.
Is there a possibility to do it all in one? To tell blast to add to every hit to which kingdom it belongs and to have then the possibility to extract e.g. all metazoan hits?
And what about sequences that return ambiguous hits e.g. hitting against metazoa and fungi? How do I deal with that ones?