Filter features for core microbiome taxa barplots

User Support
1

Hi!

I'm trying to create taxonomic barplots comparing the core microbiome of skin and gut samples. I'm trying to follow the script posted in the topic here, More complex Core Microbiome but it's producing an empty bar plot, I suspect that the qza table I'm getting from running feature-table filter-features is empty as well. As I understand, the IDs in the metadata file should be retained, am I excluding them instead?

Here's my script and outputs so far, thanks!

qiime feature-table filter-features
--i-table gut-table.qza
--m-metadata-file core-features-0.800-gut.tsv
--o-filtered-table table-core-gut-0.800.qza

qiime taxa barplot
--i-taxonomy taxa/classification.qza
--i-table table-core-gut-0.800.qza
--m-metadata-file metadata.txt
--o-visualization barplot-core-gut-0.800-only.qzv

gut-table.qza (359.3 KB)
table-core-gut-0.800.qza (154.2 KB)
barplot-core-gut-0.800-only.qzv (440.3 KB)

2

Hello @jessimya,

The filter-features command retains by default. If you also share your metadata file we'll be better able to help.

1 Like
3

Thanks for your help! I linked my metadata files below.
I think it might be having issues because the gut-table.qza (filtered from my deblur output) only has feature ID, not taxonomy, and the metadata file I'm using to filter only has the taxonomy.

core-features-0.800-gut.tsv (1.8 KB)
metadata.txt (16.5 KB)

5

Hello @jessimya,

See if the qiime taxa filter-table command fits your needs.

1 Like