Is there a compute_core_microbiome.py equivalent for QIIME 2? A search didn’t turn up anything. It was great to use in QIIME 1. Thanks!
Perfect. That looks like the equivalent! Thanks
Follow up question: previous command in QIIME 1 could run this from the tutorial website http://qiime.org/scripts/compute_core_microbiome.html
Identify the core OTUs in otu_table.biom, defined as the OTUs that are present in all of the samples in the ‘Fast’ treatment (as specified in the mapping file). Write the list of core OTUs to a text file.
compute_core_microbiome.py -i otu_table.biom -o otu_table_core_fast --mapping_fp map.txt --valid_states “Treatment:Fast”
I don’t see an equivalent in core-features. Is there a way to specify mapping file categories to look at?
This sounds like a handy option to have! Not sure if that is directly available using the
core-features function yet. While you wait for one of the expert’s to confirm that, I can suggest a couple of alternative (though not very graceful) ways to get what you want.
You can create a new feature table with only the samples from the treatment group of interest using the
feature-table filter-samples function as shown in this tutorial here. Once you have that new feature table you can simply run the core features function with whatever fraction setting you need on the new table.
Alternatively, if you are more comfortable with the qiime1 workflow for this option, you can export your biom table and carry out those commands in qiime1. The downside to this is if you decide to re-import anything back to qiime2 they will be missing the previous provenance attached to them.
Hope that helps!
Thanks @Mehrbod_Estaki - I think your approach is consistent with what I would recommend in this case. @CarlyRae, you could also
group your feature table using your metadata - YMMV. Let us know how that works out for you!
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