Hi,
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,
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.