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picrust / picrust2

Code, unit tests, and tutorials for running PICRUSt2
GNU General Public License v3.0
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seq.qza and not fna #208

Closed gafnialmog closed 3 years ago

gafnialmog commented 3 years ago

Hi,

I am intrested in testing the picrust2 toturial an my own data, this time i am not using the QIIME 2 plugin.

To do so, I need a biom table and a seq.fna , However the "moving picture toturial" on qiime2 produces qza files noly.

Can i modify this script to use qza? place_seqs.py -s study_seqs.fna -o placed_seqs.tre -p 1 --intermediate placement_working

Or can I convert qza to fna?

What do I need to do to get the files needed?

*Maybe a diffrent possiblty is to use the inffered tree rooted or unrooted by converting the rooted-tree.qza to a tre format?

gavinmdouglas commented 3 years ago

Hey there,

.qza files are compressed zip files that contain the actual files. They are in this format to keep the provenance, but you can get the actual raw files by exporting them as shown here: https://github.com/LangilleLab/microbiome_helper/wiki/Amplicon-SOP-v2-(qiime2-2020.8)#10-exporting-the-final-abundance-profile-and-sequence-files

Hopefully that helps!

Gavin