Targeted Gene Metagenomic Data Analysis    ◾    295

qiime taxa filter-table \

--i-table dada2/table_feat_sample_freq_filtered_yoga_dada2.qza \

--i-taxonomy taxonomy/nb_tax_yoga_dada2.qza \

--p-include p__\

--o-filtered-table dada2/table_phylum_yoga_dada2.qza

qiime taxa barplot \

--i-table dada2/table_phylum_yoga_dada2.qza \

--i-taxonomy taxonomy/nb_tax_yoga_dada2.qza \

--m-metadata-file data/sample-metadata.tsv \

--o-visualization taxonomy/nx_phylum_yoga_dada2_barplot.qzv

qiime tools view taxonomy/nx_phylum_yoga_dada2_barplot.qzv

Assume that you intend to explore the species under the “p__Bacteroidetes” phylum. Thus,

you can use “p__Bacteroidetes” to retain the features that contain this.

qiime taxa filter-table \

--i-table dada2/table_feat_sample_freq_filtered_yoga_dada2.qza \

--i-taxonomy taxonomy/nb_tax_yoga_dada2.qza \

--p-include “p__Bacteroidetes”\

--o-filtered-table taxonomy/table_Bacteroidetes_yoga_dada2.qza

qiime taxa barplot \

--i-table taxonomy/table_Bacteroidetes_yoga_dada2.qza \

--i-taxonomy taxonomy/nb_tax_yoga_dada2.qza \

--m-metadata-file data/sample-metadata.tsv \

--o-visualization taxonomy/nx_Bacteriodetes_yoga_dada2_barplot.

qzv

qiime tools view taxonomy/nx_Bacteriodetes_yoga_dada2_barplot.qzv

A metagenomic study may have a specific design such as groups, treatment, and facto-

rial design. The groups are to be specified in the sample metadata file as discussed above.

Grouping samples in an analysis by a group or multiple groups can be achieved by “feature-

table group”. The following script creates a feature table in which the samples are grouped

by the “group” column of the sample metadata file:

qiime feature-table group \

--i-table dada2/table_feat_sample_freq_filtered_yoga_dada2.qza \

--p-axis sample \

--m-metadata-file data/sample-metadata.tsv \

--m-metadata-column group \

--p-mode sum \

--o-grouped-table taxonomy/groupedby-group-yoga-table.qza

You can then create a barplot visualization for the new feature table; however, you need to

create a new metadata file in which the group levels (the metadata column which was used

for grouping) will be as sample ID. The metadata “taxonomy/group_metadata.tsv” will be

as in Figure 7.17.