Getting a biom file from online PICRUSt

[Heidi Smith]

Greetings,
I was wondering if a .biom file could be generated from the online version of PICRUSt. When I get through the final step online (catagorize by function) I end up with a .picrust file. I would like to generate a .biom file for downstream analysis programs.
Thank you!
-Heidi

[Romain Maleysson]

Hi Heidi,

When using categoryze_by_function.py, I get files in tab format, that I can open whith a simple text editor or with an Excel-like program. Did you check what's in the .picrust file when you open it?

You mention you did this final step 'online', I suppose you mean with the Galaxy instance available at Huttehower lab? I'm on the categoryze_by_function tool and I see a box "Type of output", did you tried it?

However, even if you don't get a biom file with the online tool you can convert it using this command :

biom convert -i your_picrust_file -o output.biom --to-json --table-type "OTU table"

"--to-json" option wile make a biom version 1.0 file (compatible with PICRUSt), you can replace it with "--to-hdf5" to get biom version 2.0 file.

"OTU table" can also be one of the following "Pathway table", "Function table", "Ortholog table", "Gene table", "Metabolite table", "Taxon table".
To do so you'll need to install the biom package on your Linux system, information available at http://biom-format.org/

Hope this helps.

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[Heidi Smith]

Thank you Romain,
I was able to convert the picrust output (which is only able to be downloaded as a .picrust file) using your biom convert. I have attached the file that I generated as I can not get STAMP to generate a stamp profile with it. Does this file look correct to you? It is only for 1 sample.
Thank you very much,
Heidi

[Romain Maleysson]

The file you send is a correct biom file, as I can reverse convert it to tab format using biom package. Is your problem solved?

To get STAMP analysis, I didn't saw your .picrust file but I bet you can use it, associated with a simple text file which specifies what kind of samples you have. Something like :

Sample       Phenotype

Wais          x

Wais2        y

With fields separated by tabulation. This webpage of PICRUSt gives some advices about this "group metadata file" construction.

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