How to combine Feature Table with the taxonomy class

[cyy]

Hallo everyone!
I have convert the feature table which form with qiime2.2019.7 from .biom to .txt by biom, like this:

Now I want to use STAMP to analyze my data. But the data that STAMP needs must be like this

that include taxonomy class and the form must be strictly hierarchy.
Please tell me how to get the right form data that STAMP could use.
Thanks very much!!!

[jwdebelius (Justine Debelius)]

Hi @cyy,

I would export your data to a biom file, export your taxonomy to a tsv, combine them, and then convert to a text file. I'll put those commands below.

However, my unsolicited reply is also to strongly discourage the use of STAMPS. It's taxonomic comparisons are based on tests that aren't appropriate for microbiome data (the user manual shows anova(!!!!) as a possible statistical test which makes all kinds of assumptions that got thrown out 2014-2017). There are a couple of posts that list some issues; here's one that links to about half a dozen more posts:

Use of rarefacted Table

Hi @m_max, Welcome! There's been a fair bit of discussion around rarefaction here (or maybe Im just involved in a lot of them). It's maybe good to go look into those threads since they'll give you a wide variety of view points. Here are a few to start that I found pretty quickly. Best, Justine

Normalization for microbiome 16s sequence analysis

@Nicholas_Bokulich thanks! Regarding the rarefaction, does the waste not want not idea not apply to that metric? I tried googling for QIIME2 normalization and found the normalize_table.py script and differential_abundance.py script. Both have options to use DeSeq normalization. There are also some 3rd party scripts implementing percentile normalization that have been developed: I couldn’t find one that does ANCOM. Is ANCOM normalization implemented in QIIME2? I’m not fully versed, but it…

You can use ANCOM, which is compositionally aware, within QIIME 2, which I might recommend as a starting point.

And, that warning issued, here's hwat I would do:

1. Export feature table to a qza. Im going to assume your feature table is called feature-table.qza

qiime tools export \
 --input-path feature-table.qza \
 --output-path feature-table

2. Then export your taxonomy

qiime tool export \
 --input-path taxonomy.qza \
 --output-path taxonomy

3. Open the taxonomy and change the header. When you open it, you'll see the header looks like this:

Feature ID	Taxon	Confidence

where the spaces are tabs. You need to change it to this:

#otu-id	taxonomy	Confidence

4. Add the metadata to the biom table

biom add-metadata \
 --input-fp table/feature-table.biom \
 --observation-metadata-fp taxonomy/taxonomy.qza \
 --output-fp biom-with-taxonomy.biom

5. Export the biom table to text

biom convert \
 --input-fp biom-with-taxonomy.biom \
 --output-fp biom-with-taxonomy.tsv \
 --to-tsv \
 --output-observation-metadata \
 --header-key taxonomy

6. Carefully edit the file according to your needs, wants and desires. If you're using excel, you want to open AS TEXT. Alternatively I would recommend python, R, or another text-handling programatic software of your choice. (Although if you're using Python, I suggest the python API for both biom and , since they're going to be easier.)

And , you now have a tax with taxonomy that is appropriate for all sorts of other visualisation software but probably shouldn't go into stamps for the aforementioned reasons.

Best,
Justine

[msport469 (Mike Sportiello)]

Thanks, but I keep getting the error that “Error: no such option: --output-observation-metadata”

What should I use instead?

[jwdebelius (Justine Debelius)]

Hi @msport469,

Could you post your commands to show the way you’re getting there?

Best,
Justine

[msport469 (Mike Sportiello)]

Hi, I found my mistake. Thanks.

[thermokarst]

@msport469, it would be very helpful for future readers of this thread if you posted your solution - thanks!