taxonomy table tsv

Hello qiime-wizers!!

I'm trying to export my filtered table from dada2 with the assigned taxonomy instead of the ASV-ID...

I'm using the following script to export the table from dada2 (after filter some unnassigned...), and convert it from biom to tsv:

qiime tools export --input-path dada2/table5.qza --output-path exported-table

biom convert -i exported-table/feature-table.biom -o exported-table/feature-table.tsv --to-tsv

However, I don't want the id of the asv... I want to download the assigned taxonomy with the counts for each sample...

Hoy can I do it??

Thank you in advance...



Did you collapse your feature table after dada2 and all the filtering to certain taxonomy level?


No, but it was not necessary because I used --p-mode exact method, so I didn't loose more than I expected...

I mean, you are trying to export already collapsed table to get taxonomy instead of ASV IDs?

No, I didn't know that u must collapse prior to export it... So what should I do after filter the dada2 table??

Right after dada2 you will have a table with ASV IDs instead of taxonomy. If you want to have a table with taxonomies instead of ASV IDs, then you should collapse it to certain taxonomy level (6 for genera). It will pool all ASVs counts, assigned to one taxa to 1 unit. When exported, it will produce a tsv file with counts for each taxon.

The same one can obtain from taxonomy barplot visualization - just download the csv table from required taxonomy level.

I already tried from the taxa_barplot, but when I try to visualize it in excel is completely messy... is there some script to organize it just like one column with the taxonomy (k_Bacteria;p_Proteobacteria...) and the one column with the counts for each sample??

No, I guess it up to user to organize the matrix in appropriate strucrure.
There are just some additional columns from the metadata file that can be deleted if not needed.


Ok I solved it, is just a problem of format csv in excel...

just in case someone would need it in the future I used:

sed -E 's/("([^"]*)")?,/\2\t/g' level-7.csv > level7.tsv

And I can open it with excel now

Thank you!

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