relative abundance

Hello everyone,
I am using qiime2 V 2021.2.
I know how to run relative abundance by this link but this method Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample as it's written in the link. but I need to determine the bacteria with abundance more than 1% among all of the samples in whole data. how can I do that?
thank you very much

To get it, you can convert a feature table (frequency) to relative table as you already know and filter this table indicating min frequency 0.01 (1%).

Or use this plugin to filter frequency table directly.

thank you. but if I convert to relative abundance, then the relative values will be based on each sample not whole data.

Technically, you can add a new metatadata column, in which all samples will have the same value, then use group plugin to group your feature table into one grouped sample and "sum" all features in the process, then convert it to the relative table and filter as needed.

But, in my opinion, the approach I already described in a previous comment would be the right one. However, I do not know your intentions, so hopefully it is what you asked for.

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.