I would like to know what is the difference between the two approches(qiime taxa collapse / biom add-metadata) for adding taxonomy annotation to the ASVs(OTUs) table.
Are both the same? is one recommended that the other?
The difference is that
collapse does not add annotation to a biom table:
$ qiime taxa collapse --help
Usage: qiime taxa collapse [OPTIONS]
Collapse groups of features that have the same taxonomic assignment
through the specified level. The frequencies of all features will be
summed when they are collapsed.
I hope that clarifies!
Thank you for your reply, I am still confused. Do you mean by the annotation the different level of taxa?
For exemple if I decide to use taxa collapse, then the further analysis on the collapsed_taxa_table.qza will be correct or I will loose some information. In my case we want to use R to analyse the table.qza file with the taxonomy annotation.
Collapse does not result in lost information, but features become merged by taxonomy and new feature IDs are assigned (the shared taxonomic lineage becomes the ID, not an annotation).
If that does not make sense, I recommend that you follow both protocols, export to TSV, and look at the differences. These methods are NOT analogous to each other.
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