Id filtered table has no features?

[swillyb]

Hello,

I removed some IDs from the table, as I wanted them out of some downstream analyses, but now Im told I dont have any features in my id-filtered-table.qza. When I open the filtered table there are definitely IDs in it. Im not sure what went wrong. Here is the file,

id-filtered-table.qza (43.6 KB)

its probably an easy fix, but Im new to deeper analyses with qiime beyond just making bar plots, thanks so much fro your help!

[ebolyen (Evan Bolyen)]

Hi @swillyb,

It appears that your table is in fact empty. Running biom summarize table on the contents of that qza gave me this:

Num samples: 0
Num observations: 0
Total count: 0
Table density (fraction of non-zero values): 0.000

Counts/sample summary:
 Min: 0.000
 Max: 0.000
 Median: 0.000
 Mean: 0.000
 Std. dev.: nan
 Sample Metadata Categories: None provided
 Observation Metadata Categories: None provided

What was your filtering command (and associated file which you used to filter by)?

[swillyb]

oh ok, then I clearly did this wrong.

I was trying to follow the identifier based filtering and I used the taxonomy.tsv, opened that and removed some of the rows, saved that as samples-to-keep.tsv, then ran

qiime feature-table filter-samples
--i-table table.qza
--m-metadata-file samples-to-keep.tsv
--o-filtered-table id-filtered-table.qza

here is that file

samples-to-keep.tsv (52.2 KB)

... im guessing this was not correct ...

[ebolyen (Evan Bolyen)]

Hi @swillyb,

I see the problem. You’re using feature metadata (taxonomy.tsv) to filter samples. Since none of the feature IDs match your sample IDs, there’ll be nothing left “to keep”.

If you use feature-table filter-features I think the command will do what you expect

[swillyb]

ok great!

Im still a bit confused, sorry!

The table.qzv has feature IDs, but I cant download this as a .tsv, and none of the taxonomic identifications are present when I visualize it.

What I would like to do is remove all of one genera from the data and generate bar plots, and do differential abundance analyses etc. with that one genera removed… does that make sense?

thanks so much for your help here, its very much appreciated!

[Nicholas_Bokulich]

@swillyb

The table.qzv has feature IDs, but I cant download this as a .tsv, and none of the taxonomic identifications are present when I visualize it.

You will need to export table.qza to biom format, then convert to tsv if you really need this in tsv format.

If you are trying to export this table for use outside of QIIME 2 (e.g., with phyloseq), see this tutorial.

But it sounds like maybe that's not what you really want.

@swillyb

What I would like to do is remove all of one genera from the data and generate bar plots, and do differential abundance analyses etc. with that one genera removed… does that make sense?

Ah, yes, that makes lots of sense. You will want to use filter-table — see this tutorial.

I hope that helps!

[swillyb]

Thank you so much!! this worked!!