modification of taxonomy.qza

Other Bioinformatics Tools
1

Hi,
Is there a way we can separate the taxonomy column in taxonomy.qza file into separate columns each for phylum, class, order, family, genus and species. I need this format for using in BURRITO.
Can anyone who has used BURRITO earlier suggest how to use it.

2

You can simply export the TSV file like so:

qiime tools export \
  --input-path taxonomy.qza \
  --output-path exported-taxonomy

Then open the taxonomy.tsv file within the exported-taxonomy folder and edit as required. There are formatting examples here. I pasted their Greengenes-like example below:

OTU Kingdom Phylum
OTU1_ID k__Bacteria p__Bacteroidetes
OTU2_ID k__Bacteria p__Bacteroidetes
OTU3_ID k__Bacteria p__Firmicutes
OTU4_ID k__Archaea p__Euryarchaeota

I assume this will work with SILVA too? :man_shrugging:

I'd imagine you can simply use a basic text editor like BBEdit, etc.. and replace all ; with \t (tab) characters. You may need to remove spaces too.

2 Likes
3

Thank you for your suggestions. I edited the taxonomy.tsv file as you suggested.

4

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