PICRUSt workflow - LangilleLab/microbiome_helper GitHub Wiki

First reduce OTU table to just the reference OTUs. Note that the path to the reference below is for the latest version of our virtual box, you may need to swap out the path to something like "/usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta".

filter_otus_from_otu_table.py -i final_otu_tables/otu_table.biom -o final_otu_tables/closed_otus.biom --negate_ids_to_exclude -e /home/mh_user/anaconda2/envs/qiime1/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta

PICRUSt: normalize OTU table by predicted 16S copy numbers.

normalize_by_copy_number.py -i final_otu_tables/closed_otus.biom -o final_otu_tables/closed_otus_norm.biom

PICRUSt: Predict abundances of KEGG orthologs (KOs) in each sample.

predict_metagenomes.py -i final_otu_tables/closed_otus_norm.biom -o final_otu_tables/ko.biom

PICRUSt: Collapse KOs into KEGG Pathways.

categorize_by_function.py -i final_otu_tables/ko.biom -l 3 -c KEGG_Pathways -o final_otu_tables/ko_L3.biom

Convert BIOM to STAMP format. Note that if you wanted to convert the KO table (ko.biom, the output of predict_metagenomes.py above) rather than the KEGG pathways you would just need to change the -m option to "KEGG_Description".

biom_to_stamp.py -m KEGG_Pathways final_otu_tables/ko_L3.biom > final_otu_tables/ko_L3.spf

Note: If you are using PICRUSt 1.0.0 then you will need to make sure you are using BIOM 1.3.1 (and not the newer BIOM 2.1.*). This is not an issue with the newer PICRUSt versions.

To get around this you can:

Install BIOM 1.3.1 and temporarily change your PYTHONPATH (after #2 above)

pip install --target ~/lib biom-format==1.3.1
export PYTHONPATH=~/lib/

And then revert back to newer BIOM version by exiting and logging back into the shell or (after #5):

export PYTHONPATH=''

Also, if you are using v1.0.0, you will need to convert to JSON BIOM format before running PICRUSt:

biom convert -i final_otu_tables/closed_otus.biom -o final_otu_tables/closed_otus_json.biom --to-json --table-type "OTU table"