QIIME OTU-picking: doubles counts or not?
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5.7 years ago
lotus28 ▴ 70

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?

qiime metagenome otu-picking mapping • 1.2k views
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