diversity and taxonomy analysis with combined feature table and taxonomy.biom file

[Barandouzi (Zahra Barandouzi)]

Hello,

I combined “feature-table.biom” file and “taxonomy.biom” file and I was wondering if you could please let me know about the next step for diversity and taxonomy analysis. Do I still need to do quality control?

Also, please let me know how can I convert “biom” file to “qza”?

Thanks,
Zahra

[SoilRotifer (Mike Robeson)]

Hi @Barandouzi,

@Barandouzi

if you could please let me know about the next step for diversity and taxonomy analysis. Do I still need to do quality control?

Check out our tutorials here.

@Barandouzi

how can I convert “biom” file to “qza”?

This is outlined in the import documentation. Be sure to check which biom format you are using, i.e. 1 or 2.1.

[Barandouzi (Zahra Barandouzi)]

Thank you for your reply. I just finished tutorial. But I did not see any instruction about analyzing “biom” file with combined feature table and taxonomy. Also, in “import documentation”, there was no instruction on converting taxonomy.biom to qza (it is just about converting feature table). I have a more question about converting tsv to qza. I just want to know how we can do it.

Thanks!
Zahra

[SoilRotifer (Mike Robeson)]

@Barandouzi

But I did not see any instruction about analyzing “biom” file with combined feature table and taxonomy.

You may have noticed that QIIME 2 differs from QIIME 1 in some respects. One of these differences is that the feature-table (i.e. OTU-table) is kept separate from the taxonomy data. That is, there is no single file that will contain both the OTUs / ASVs and the taxonomy. This has to do with the type system, and to keep things modular. If you look through the "Moving Pictures" tutorial, you'll see that some commands require both a feature and taxonomy data as inputs. For example, to make a barplot you have to provide these two files:

qiime taxa barplot \
  --i-table table.qza \
  --i-taxonomy taxonomy.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization taxa-bar-plots.qzv

You'll have to export your biom data as a TSV file you'll find many examples of how to do so with the biom convert command. For example:

biom convert -i table.biom -o table.from_biom.txt --to-tsv

You can look through the forum to see how others have imported these and other file types. For example, here is how to import a taxonomy.tsv file.

You can also import both parts of the biom table (OTUs and Taxonomy) like this.

-Cheers!