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?
Welcome to the forum, @Yeong
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.
Thanks for your reply.
I used biom convert after collapse. (like below)
biom convert –i feature-table.biom –o rel-phyla-table.tsv –to-tsv
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.
It shows 0.005021, 0.002051 etc. (<1)
I guess it means relative abundances, am I right?
Yeap, If you have some doubts - make a sum of all frequencies for each sample in excel or R/Python and see if the will give you 1 (ratios) or 100 (%).
Thank you so much timanix!
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