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.
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?
I'd imagine you can simply use a basic text editor like BBEdit, etc.. and replace all
\t (tab) characters. You may need to remove spaces too.
Thank you for your suggestions. I edited the taxonomy.tsv file as you suggested.
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