Visualising PICRUSt2 output in Stamp

[Alan Hudson]

Hi, 

I ran the PICRUSt pipeline and would like to visualise the results in STAMP to identify functional differences in the microbiome among treatment groups. I read on one of the group postings that the results would need to be normalised taking into account the sample read counts first, before importing into STAMP. However, I am not sure which of the output files would need to be normalised and the best way of actually normalising the data

Would the "biom_to_stamp.py" script accomplish this?

I asked a similar question on the PICRUSt google groups. Any advice on how best to do this would be very gratefully received!

Alan

[Gavin Douglas]

Sorry for missing your message on the PICRUSt2 google group - you can see my response here: https://groups.google.com/g/picrust-users/c/otuOAFpu1s8/m/pL977egNDQAJ?utm_medium=email&utm_source=footer

The unstratified gene family or pathway tables would be the key files to visualize.

The biom _to_stamp.py script is for biom files specifically, which is a different format then the output TSV files produced by the standalone PICRUSt2 tool.

Cheers,

Gavin

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