how to do the alpha and beta diversity and microbiota composition analysis ?

[timanix (Timur Yergaliyev)]

Hi again!

@terren

qiime feature-table group
–i-table table-dada2.qza
–p-axis sample
–m-metadata-file sample-metadata.tsv
–m-metadata-column trea-line
–p-mode sum
–o-grouped-table grouped-table.qza
–verbose

You summarized frequencies from all samples in group - is it by purpose? I would recommend to redo it with

mean-ceiling will take the ceiling of the mean of these frequencies;

or

median-ceiling will take the ceiling of the median of these frequencies.

@terren

Then I used the following commands to generate bar-plots, but it failed.

Last time I run this command for cllapsed tables I encountered an error as well. It was solved by creating a new metadata file, in which I had only groups instead of samples id's.
So, if you have only two groups, your new metadata file should contain only two 'samples' - your groups.