Per read assignment

Hey Guys,

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?


Hi @Bhav_Verma
Thanks for getting in touch. As you mention, the MetaPhlAn database only contains the species-specific marker genes (maximum 150 genes per species), so the numbers you are reporting are totally expected.