taxonomy table tsv

Technical Support
1

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...

Sincerely,

Ana.

2

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

3

Hi!

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

4

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

5

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

6

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.

7

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??

8

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.

Best,

10

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!

11

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