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Code, unit tests, and tutorials for running PICRUSt2

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Gene family abundances per ASV rather than per sample

antonkratz opened this issue · comments

commented

A different approach would be to look at the predicted genomes of ASVs generated by the hidden-state prediction step (which represents the gene family abundances per ASV rather than per sample).

I am seeking gene family abundances per ASV rather than per sample. I ran my analysis using the wrapper script like this:

picrust2_pipeline.py --stratified -i exported_table/feature-table.biom -s exported_seqs/dna-sequences.fasta -o picrust2_out_pipeline2 -p 1

Where can I find the the predicted genomes of ASVs generated by the hidden-state prediction step?

commented

Hi there,

You can find the per ASV predictions in EC_predicted.tsv - this shows how many copies of each EC number are predicted to be in each genome.

Robyn