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My first guess would be that a lot of predicted abundance is assigned to "Genus_unclassified" levels. These don't have pangenomes in HUMAnN2 to be selected, hence the abundance of the selected pangenomes adds up to a lot less than 100%.Thanks,Eric
On Wed, Jan 15, 2020 at 3:40 PM adamber1187 <adam.be...@gmail.com> wrote:
Hello all,--I'm running HumanN2 with shotgun metagenome samples (150 bp). On the Metaphlan2 step the amount of species for my first sample is 81, but only explains 30.78% of predicted community composition. The input is about 5.5 million base pairs. Just curious why the amount explained is so low? When I've done this in the past it's usually 99-100%.Thanks in advance,Adam
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