collapse taxa(example genus)
qiime taxa collapse
–i-table table.qza
–i-taxonomy taxonomy.qza
–p-level 6
–o-collapsed-table table-collapsed-L6.qza
check the number of features per taxa:
qiime feature-table summarize
–i-table table-collapsed-L6.qza
–o-visualization table-collapsed-L6-summarize.qzv
–m-sample-metadata-file sample-meta.tsv
now we do diversity core-metrics (do not miss with core-metrics-phylogenetic)
qiime diversity core-metrics \ --i-table table-collapsed-L6.qza \ --p-sampling-depth 1125 \ --m-metadata-file sample-meta.tsv \ --output-dir core-metrics_no-phylogenetics
and now we can look on PCoA:
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