Error in my Feature Table with Taxonomy .tsv

Hello again,

I'm trying to get a feature table with taxonomy annotation so I can run several downstream analysis, so I followed all the steps wrapped up by @thermokarst on the following post: Exporting and modifying BIOM tables (e.g. adding taxonomy annotations)

Everything seems ok and I didn't run through any errors, but when I open my feature-table-withtaxon.tsv everything is messed up. I'll attach the files here so you can have a look what I'm talking about.

Thank you,
Felipe.

biom-taxonomy.tsv (1.1 MB) feature-table.tsv (1.4 MB) feature-table-withtaxon.tsv (1.5 MB)

Hello @Felipe_Rocha,

The command @thermokarst ran was meant to produce a .biom file not a .tsv file. I suspect you followed all the steps correctly, but gave your output file, feature-table-withtaxon.tsv, the wrong file extension. It should be a valid .biom file, but when viewed as a .tsv it looks corrupted and broken because .biom is a binary file format. Please change the extension on the file from .tsv to .biom and let us know if it works in your analyses.

Thank you,
@Oddant1

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Hi @Oddant1,

thank you so much for the answer. That was indeed the problem, right in front of my eyes ARRGH!
It worked and I got a feature table with taxonomy.

The thing is that when I try to convert the table with taxonomy to .tsv, the tsv format stays exactly like it was before assigning taxonomy. I still get feature ID instead of taxonomy. I’ll have a look on some other posts, but if you have any ideas please share :smiley:

It’s worth noting that when I give the command: biom head -i feature-table-withtaxon.biom, I get feature ID also, and not the taxonomy. So the problem is not on the conversion, but somewhere in assigning taxonomy?

Thank you for your help,
Felipe.

Hello @Felipe_Rocha

I notice your feature table is also a .tsv, did you use this .tsv in the command you ran when attempting to create your annotated feature table? If so, please try again using the original feature-table.biom file.

Note that this time changing the file extension on that file from .tsv to .biom will almost certainly not work as feature-table.tsv is an actual .tsv, and you will need the original feature-table.biom you created before transforming it into a .tsv.

Thank you,
@Oddant1

Hey,

No, after your first reply I used the feature-table.biom to create my feature-table-withtaxon.biom following the steps provided by @thermokarst. But when I run biom head -i feature-table-withtaxon.biom I still get a table with Feature ID, and not taxonomy.

Thanks,
Felipe.

These are my commands:

(qiime2-2019.4) [email protected]:~/Documents/Felipe-Seq/Exported-FelipeChelifer-FeatTable$ biom add-metadata -i feature-table.biom -o feature-table-withtaxon4.biom --observation-metadata-fp biom-taxonomy.tsv --sc-separated ‘taxonomy’

(qiime2-2019.4) [email protected]:~/Documents/Felipe-Seq/Exported-FelipeChelifer-FeatTable$ biom head -i feature-table-withtaxon4.biom

Constructed from biom file

#OTU ID CN3 P23C P28C P38C C39C
2ca9258b7350961759ee32c679b9d92a 0.0 0.0 0.0 0.0 0.0
8ca1d3d61ed01004612a8457a8b7b839 0.0 0.0 0.0 0.0 0.0
39b8827b8dbc27d3fb7c001d46d219e7 0.0 0.0 0.0 0.0 0.0
121bd57672d7fe719f07e08f701b7fee 0.0 0.0 0.0 0.0 0.0
29e4dde5513153801b9403ec372403d8 0.0 0.0 0.0 0.0 0.0

Please run the following, instead:

biom summarize-table -i feature-table-withtaxon.biom

What does the section titled “Observation Metadata Categories” say? You should see “confidence; taxonomy”

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Yes, that is exactly what it is showing! Does it mean that I got my taxonomy now?

I see that I’m getting exactly the same thing as this other post here: Biom add-metadata problem

I think there is no solution for now, but I was really forward to use the feature table on R. If you guys know anything, please, let me know!

Thanks,
Felipe.

Yes, the taxonomy is included as “metadata”. Please see the biom docs for more details:

http://biom-format.org/documentation/adding_metadata.html

I suspect you might be confusing two different concepts here: adding metadata vs collapsing

My suspicion is that you actually are looking for a collapsed feature table, collapsed on your taxonomy.

Check out this method: https://docs.qiime2.org/2019.7/plugins/available/taxa/collapse/

To see it in action: https://docs.qiime2.org/2019.7/tutorials/moving-pictures/#differential-abundance-testing-with-ancom (there are steps within this ancom section that demonstrate table collapsing).

Once you have collapsed your feature table, you can export it.

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Oh well, you got me! I was confusing these two different concepts :cry:

I already had many different tables with collapsed taxonomy, but I didn’t think on using them to export. So frustrating…

I cannot thank you as much as I wanted to. Really!
Felipe.

1 Like

Glad to hear you got it sorted! I have made this same mistake myself!

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