Hello, when you run the core-metrics-phylogenetic command there is an option to set a sampling depth and thus the command is only run on a random subsample of features. Is it possible to generate a table showing which features were randomly subsampled for these core metrics along with which sample they are in. Thank you!
Hello @Brandon_Feole1 and welcome to the 
Forum!
You are looking for the rarefied feature table, which is already one of the outputs of qiime diversity core-metrics-phylogenetic. If you want to directly observe that table, you need to export the BIOM table included in the rarefied table QZA (either following the Exporting Tutorial or directly opening the QZA as a ZIP file and manually extracting it) and then use the biom convert command on the BIOM table. Probably your command will look similar to:
biom convert -i feature-table.biom -o feature-table.tsv --to-tsv
If you have trouble converting the BIOM file, maybe you find this post useful.
Cheers!
Sergio
3 Likes
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.