How to make rarefied taxonomy tables at each taxonomic level?


I am trying to make rarefied taxonomy tables at each taxonomic level but I cannot find the way to do it (I am only able to make a taxonomy table without rarefaction).
Could you please tell me how to make it?

Thank you so much for your help!

Hi @scho73!

You can rarefy your table by running feature-table rarefy (you will need to update this match your file names and desired sampling depth):

$ qiime feature-table rarefy \
  --i-table my-table.qza \
  --p-sampling-depth [SAMPLING DEPTH] \
  --o-rarefied-table my-rarefied-table.qza

Then, to collapse at different taxonomic levels, please take a look at taxa collapse, which will collapse a table (rarefied or not) based on a specified taxonomic level via a provided taxonomy artifact:

$ qiime taxa collapse \
  --i-table my-rarefied-table.qza \
  --i-taxonomy taxonomy.qza \
  --p-level 3 \
  --o-collapsed-table my-rarefied-table-at-level-3.qza

An example of this in the Moving Pictures tutorial can be found here: EXAMPLE.

Please let us know if we can provide any additional help. Thanks!


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