How to convert .picrust format to tsv using Galaxy?

[EJT]

Hello,

I have successfully run the PICRUSt functions in Galaxy, however I'm unsure how to convert the output (.picrust, picrustn, etc.) to a format I can use (txt, tsv, biom). How do I do this if I'm using Galaxy?

Thank you very much,

Emily

[Julia Cope]

Emily,

There are two options. To stay in the galaxy server you may redo the
analysis in Galaxy and choose QIIME Legacy as the output (this will be
a tab delimited table). The second is that you can use a BIOM
converter on your own machine to change the biom files to text files
of the same tab delimited format. The file endings may be non-standard
but the formatting will be accessible.

The legacy files are easy to open in any spreadsheet program and edit
to fit your favorite flavor of statistical programs or image
generation pipelines. I do not suggest outputting qiime legacy files
for use with other PICRUSt steps as I have seen the galaxy PICRUSt
instance choking on classic QIIME files in subsequent steps. I hope
this helps.
-Julia

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--
Julia Cope, Ph.D.
Department of Pathology
Baylor College of Medicine

[EJT]

Julia,

Thank you! This did the trick for predict metagenome and categorized by function files. Is there a way to choose the output for the normalized by copy number files also?

Thanks again.

Emily

[Julia Cope]

Emily,

Not that I know of. (But if you used qiime to pick OTUs, you have a biom converter.)

-Julia

[EJT]

Thanks Julia, I'll check that out.

-Emily