STAMP file preparation problem

[Md.Ishtiak Rashid]

Hi all

I've completed PICRUSt2 standalone analysis and now want to use STAMP. I tried to follow this tutorial :https://github.com/LangilleLab/microbiome_helper/wiki/STAMP-preparation.

However, I'm not sure about the input file for the STAMP since I'm facing error running the codes below and which file is exactly the 'feature-table_w_tax.biom' file. Because, the feature-table.biom that I have, doesn't contain the bacterial taxa information, only the pathways. Since I ran Qiime SOPs, is it possible to prepare files for stamp from there?

biom_to_stamp.py -m taxonomy \
                 deblur_output_exported/feature-table_w_tax.biom \
                 > deblur_output_exported/feature-table_w_tax.spf

fix_spf.py -i deblur_output_exported/feature-table_w_tax.spf \
           -o deblur_output_exported/feature-table_w_tax_final.spf \
           --replace_ambig_letter_format

Best,

Ishtiak

[Andre Comeau]

The wiki link/scripts you have listed below are for when you have run normal 16S analysis through QIIME2 - those files below (ie: the BIOM feature tables) would be your starting point for making the STAMP files.

You want the tutorial/instructions from the PICRUSt2 wiki: https://github.com/picrust/picrust2/wiki/STAMP-example

	ANDRÉ M. COMEAU, PhD Manager • Integrated Microbiome Resource (IMR) T: 902.494.2684 | E: andre....@dal.ca	​Address for deliveries: Dept. of Pharmacology Tupper Med. Bldg., room 5D Dalhousie University 5850 College St. Halifax NS B3H 4R2
​	Research Associate (Lab Manager) Morgan Langille Lab • Dept. of Pharmacology ResearchGate Profile • GoogleScholar Publications
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From: microbio...@googlegroups.com <microbio...@googlegroups.com> on behalf of Md.Ishtiak Rashid <shoeb....@gmail.com>
Sent: Friday, September 9, 2022 1:58 AM
To: Microbiome Helper <microbio...@googlegroups.com>
Subject: [microbiome-helper] STAMP file preparation problem

 

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