I am trying to export a table of relative abundances using “feature-table relative-abundance” but am getting an error saying that feature-table "has no action ‘relative-abundance’ ". What would be the best way to proceed using a collapsed table?
Hello!
Can you post your full command? I wonder if your command matches the syntax in the documentation.
Colin
Thank you so much for linking the documentation! I was using the command
“qiime feature-table relative abundance” instead of
“qiime feature-table relative-frequency”
This worked:
qiime feature-table relative-frequency
–i-table filtered-table-b6-day14.qza
–o-relative-frequency-table b6-day14.qza
How would I then be be able to export the output frequency table?
Good morning,
tGlad that worked!
Like as a .csv file? There are some examples over here, and I think these examples could be helpful too.
Let me know if these works for you. There are many different ways to do this, so let me know what you try.
Colin
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Those examples were really helpful! I just can’t seem to add taxonomy info to classify OTUs. I’ve tried using:
biom add-metadata -i exported-feature-table-b6-day14/feature-table.biom -o table-with-taxonomy-b6day14.biom --observation-metadata-fp biom-taxonomy.tsv --sc-separated taxonomy
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I’m glad you got this exported!
Adding the taxa info is a little finicky. Can you post a few lines of your biom-taxonomy.tsv file? Are you getting an error?
Colin
I am not getting an error.
This i what the header of my biom-taxonomy.tsv looks like. I double checked to make sure it is tab separated.
Your taxonomy file looks good to me! I’m not sure what causing this issue. Let’s see what the qiime developers recommend.
If you are not getting an error, are there any other clues to what is going wrong? What doesn’t work for you?
Colin
@Mericien_Venzon could you please clarify what you want as your end result?
@colinbrislawn and I interpreted this the same way: you want to add taxonomy information to your biom table after exporting. Thus you would have a feature table where your unique sequence variants are the observations, and they are annotated by taxonomy.
However, perhaps what you are looking for is a feature table that is collapsed on taxonomy. I.e., taxa names are the observations in your biom table.
If that's the case, check out qiime taxa collapse. You will input a feature table and taxonomy file, collapse, export, and voila.
Let us know if that helps!
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Using qiime taxa collapse solved it, thank you both!
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