Hi!
I'm a user of qiime2 for 16s amplicon sequencing data analysis.
I have a simple question.
I got my data and did the relative abundance calculation of taxonomy.
(qiime taxa collapse )
In this procedure, what is the equation of this relative abundance calculation?
Could you explain me how it works?
Did you convert absolute abundances to relative after a collapse? If not, then you have absolute abundances at certain taxonomy level.
On the collapsing step, all absolute abundances (frequencies) of ASVs (OTUs) are summarized based on taxonomy annotations.
When you are converting a feature-table to relative abundances, then counts (frequencies) of each feature (ASV, OTU, taxonomy unit) in a given sample will be divided by the sum of all counts (frequencies) of all features in a sample.
You can check it easily - if in a .tsv table you have feature counts from 0 and >, it is absolute abundances. If < 0 and all features in a sample sum up to 1 - relative abundances.
If you still have absolute one, you can convert feature table to relative by the link above before converting a biom to .tsv, or just do it in a .tsv table by dividing each count in a table by the sum of all feature counts in a given sample.