Hello,
As a very frequent user of Qiime1 it was very easy to subsample an OTU table in order to normalize it according to the lowest sample’s read depths.
Now in Qiime2 I have no idea how to do it. I have been searching on the website but it is really not clear.
I would imagine it should be a straight forward command?
Please help me out
Tamar
Hello Tamar,
Thanks for trying out Qiime 2 
Many of the qiime 1 functions have been reorganized in Qiime 2, and some things are pretty different. So for example, rarefaction is 'built in' to the qiime diversity alpha-rarefaction command in Qiime 2. Take a look at this example here:
https://docs.qiime2.org/2019.4/tutorials/moving-pictures/#alpha-rarefaction-plotting
If you just want to subsample your table, there is a plugin for that:
https://docs.qiime2.org/2019.4/plugins/available/feature-table/rarefy/
Let me know if this helps!
Colin
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