I used QIIME's
pick_closed_reference_otus.py with the latest greengenes dataset.
But I couldn't find any info on how it treats reads that can be assigned both to a species and to a genus. Does it count this read twice: adding it both to genus and to species? Or just once: adding it only to the species?
Do I need to sum all lower taxon reads and add them to the higher ones or just leave the output as it is?