I am using the qiime2-2020.8 conda version and I have used the “qiime feature-table rarefy” plug-in to rarefy an ASV table: qiime feature-table rarefy --i-table table3.qza --p-sampling-depth 5000 --o-rarefied-table table3-raref.qza
In the qiime2 docs I have read the following information about the rarefy plug-in (rarefy: Rarefy table — QIIME 2 2021.2.0 documentation): --p-with-replacement / --p-no-with-replacement
Rarefy with replacement by sampling from the
multinomial distribution instead of rarefying without
replacement. [default: False]
I was wondering what is the meaning of default: False. Does it mean that rarefaction is conducted with replacement by default?
I would like to confirm this idea since my rarefied table has a minimum depth of 5,000 reads but not every sample has the same depth (as expected using rarefaction without replacement, I assume).
This means that the default is --p-no-with-replacement, which means that by default, no replacement is performed during the rarefy command. I pulled the relevant source code up here, in case you're interested:
So if the default of the rarefy plug-in is to rarefy without replacement, how come I have obtained a table with each sample having a different total sum of ASVs but all larger than 5,000? It seems to me that the table was rarefied with replacement, right? Is it possible that the Qiime2 version I used had a different default parameter?
In any case, I just want to confirm that the table I have was rarefied with replacement. Is that correct?