Thanks for the great tool. I was wondering if I could get per read marker gene assignment.
Specifically, I have 1000000 reads but only 26000 are mapped in the Bowtie file. It’s also a similar thing with your example files on the wiki. Is it because a large subset of these reads were not mapped to marker genes?
My ideal goal would be to have a taxon and/or a marker gene per read that could be mapped to a taxon. Is this possible with MetaPhlan or should I just expect a large subset of reads can’t be mapped to a taxon?