Core-features taxonomy

Hello,

I am trying to run the command qiime feature-table core-features to identify the core microbiome, however the core features returned to me are (seems to be) encoded. How can I have the features returned to me so that I know what species/taxon these features are?

Thanks in advance.

Hi @Alan_Chan,
By encoded do you mean they are hasehd i.e. like so: 2e55763e77234a7bfc3a311067a0c7e1?
If so, these represent the exact denoised amplicon sequence variants (ASV). They are the most accurate (we think) version of your read and do not have taxonomy assigned to them.

You have 2 options, the first one is to simply blast those features by looking them up in your rep-seqs.qzv, this is a quick and dirty approach and not really useful if you want to look up lots of samples. The second and maybe better option is to assign taxonomy to your feature table prior to running core-features. You can follow the the moving pictures tutorial’s taxonomy section, and once you have your classifier you can use the 'taxa-colllapse function to assign taxonomy to your feature table, then simply run that new feature table through core-features.
Hope that helps!

6 Likes

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