OTUs from multiple regions: Greengenes fragment test results
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Can we make OTUs from different V regions?
This test uses full-length 16S sequences from the
Three different segments are extracted: V3, V4 and V3-V5 using primer pairs
commonly used in tag sequencing experiments. See
Greengenes fragment test for details.
Results are shown in the table below.
Classified is the number of genes where all three
fragments (V4, V5 and V3-V5) were classified. In the case of QIIME closed-ref,
it is notable that more than 10% are not classified, considering that the
reference database is Greengenes. This happens because the reference database is
Greengenes clustered at 97% identity rather than the full Greengenes set.
Same OTU is the number of of genes where all three
fragments (V3, V4 and V3-V5) were assigned to the same OTU.
This test should favor the QIIME closed-reference method
because the Greengenes database is used as both the query and reference set,
while UTAX uses the RDP training set as a reference. However, QIIME only
identifies 15.7% of fragments as belonging to the same gene and thus fails in
most cases (84.3%). This is consistent with the very poor results for QIIME
closed-ref on the HMP sample test where
the similarity between identical samples sequenced by different V-regions ranges
from 6.1% to 0.9%.