How to merge taxonomy.qza and table.qza using metadata tabulate?

Dear Sir or Madam:

When I input: qiime metadata tabulate --m-input-file taxonomy.qza --m-input-file rep-seqs.qza --o-visualization taxo-table.qzv, it worked fine. However, when I input: qiime metadata tabulate --m-input-file taxonomy.qza --m-input-file table.qza --o-visualization taxo-table.qzv, it did not work, with error message: cannot merge because there are no IDs shared across metadata objects. I am wondering why the ids in table.qza and repseqs.qza are not shared and how to solve this problem. Thanks in advance for your help.

This is all a matter of dataframe orientation.

When you did this:

it worked because the indices of those two files matched… both are lists of feature IDs with feature metadata like this:

species1    blah;blah;blah
species2    blah;blah;blah
species3    blah;blah;blah

But the table is in a different orientation, where the index is sample IDs like this:

sample-id species1 species2 species3
sample1 0 12 1
sample2 14 2 0
sample3 3 2 6

So you could transpose your table first, with qiime feature-table transpose prior to merging with your metadata.

Good luck!

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