In running this script
qiime diversity beta-group-significance \
--i-distance-matrix core-metrics-results/bray_curtis_distance_matrix.qza \
--m-metadata-file metadata-file.tsv \
--m-metadata-column Description \
--o-visualization core-metrics-results/bray-curtis-group-siqgnificance.qzv \
Does this perform the bray-curtis comparison and PERMANOVA at the phylum level?
Is there anyway to examine the differences at other taxonomic levels like genus?
Does qiime2 have an option to run ANOSIM instead of PERMANOVA?
Great questions! Let’s dive in.
This script just performs the permanova test on whatever distance matrix you provide. Based on the file name, this looks like a matrix of Bray Curtis dissimilarities.
By default, these are calculated at the feature level (instead of grouping by phylum or grouping by genus, then calculating these dissimilarities). I would recommend keeping it like this.
Yes! Check out the documentation to learn how, and let me know if you have any questions.
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.