How to convert otu_table.tsv (with # OTU in the 1st column and taxonomy in the last column) to otu_table.qza

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1

Hi experts,

I received the otu_table.tsv from my colleage. I am intending to use this otu_table for qiime. I would like to know how I can convert otu_table.tsv (with # OTU in the 1st column and taxonomy in the last column) to otu_table.qza without losing the last column of taxonomy,
Previously, I used the biom command to convert from tsv to biom format:
biom convert -i path_to_input.tsv -o path_to_output.biom --to-hdf5 --header-key taxonomy

After that I use qiime import to convert biom format to qza format:
qiime tools import \
--input-path feature-table-v210.biom \
--type ‘FeatureTable[Frequency]’ \
--input-format BIOMV210Format \
--output-path feature-table-2.qza

However, the output file lost the content in the taxonomy column.

Please find otu_table.tsv from this link for your reference: taxonomy_closed_reference.tsv - Google Drive

Thank you very much for your kind instructions and advice,
Kind regards,
Le Phuong.

2

Hello!
That will not be difficult. In qiime2, taxonomy stored not in the biom, but in the separate file. So all you need to do is to create a second tsv table, in which you will only have OTU IDs as a first column and a second column Taxon with taxonomy. I guess you already imported count table so you already have a feature table. Import your second table as taxonomy:

qiime tools import
  --type FeatureData[Taxonomy] \
  --input-path taxonomy.tsv \
  --output-path taxonomy.qza
3

Hi Timur,

Thank you very much for your kind instructions. I still have another concern. After I did the relative_otu.qza. I intended to convert back relative_otu.qza to relative_otu.biom and then to relative_otu.tsv. The relative_otu.tsv does not contain the taxonomy. I'd like to know to make the relative_otu.tsv with the taxonomy column.
Similarly, I used the rarefy function to make the rarefied_otus.qza. After that I converted about the conversion back from rarefied_otus.qza to rarefied_otus.biom and then to rarefied_otus.tsv. This rarefied_otus.tsv does not contain the taxonomy column.
Is there any function in qiime could help to match the taxonomy.qza and rarefied_otu.qza/relative_otu.qza together for converting to relative_otu_with_taxonomy.tsv/rarefied_otu_with_taxonomy.tsv?

Thank you very much,
Kind regards,
Le Phuong.

4

In that case I think the best option will be to add taxonomy at the very end of yoour operations, when you have ready tsv tables. I would use R or Python to do the job rather than adding it manually.

5

Hi Timur,

I understood, which you suggest the command line to do in R,
Thank you very much,

Kind regards,
Le Phuong Nguyen.

6

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