I have built an OTU table using the instructions above. Now I have my study participants as columns and OTUs as rows. I would also like to build a picrust2 table. I am overwhelmed by the tutorials. Is there an easy way to get a picrust2 processed table of functional abundances? I think I might have already many of the missing pieces in place, but how can I specifically built a functional abundance table with picrust2?
Basically, I have built my OTU table from pared-end V4 fasta like this:
qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path ${location_path}Taxonomy_Classification/qiime_manifest.tsv --input-format PairedEndFastqManifestPhred33V2 --output-path ${prj_name}.qza
qiime demux summarize --i-data ${prj_name}.qza --o-visualization ${prj_name}.qzv
qiime dada2 denoise-paired --p-n-threads 0 --i-demultiplexed-seqs "${prj_name}.qza" --p-trunc-len-f $fwd_read --p-trunc-len-r $rev_read --output-dir DADA2 --verbose -p-pooling-method 'pseudo' &> DADA2_denoising.log
qiime feature-table summarize --i-table table.qza --o-visualization table.qzv
qiime metadata tabulate --m-input-file denoising_stats.qza --o-visualization denoising_stats.qzv
qiime feature-table tabulate-seqs --i-data representative_sequences.qza --o-visualization rep_seqs.qzv
qiime feature-classifier classify-sklearn --i-classifier $classifier_path --i-reads representative_sequences.qza --o-classification "${location_path}Taxonomy_Classification/analysis/taxonomy/classified_rep_seqs.qza" --p-n-jobs 6
qiime metadata tabulate --m-input-file classified_rep_seqs.qza --o-visualization classified_rep_seqs.qzv
qiime taxa barplot --i-table "${location_path}Taxonomy_Classification/analysis/DADA2/table.qza" --i-taxonomy classified_rep_seqs.qza --m-metadata-file "${location_path}Taxonomy_Classification/qiime_metadata.tsv" --o-visualization "${location_path}Taxonomy_Classification/analysis/outputs/taxa-bar-plots.qzv"
qiime taxa collapse --i-table "${location_path}Taxonomy_Classification/analysis/DADA2/table.qza" --i-taxonomy classified_rep_seqs.qza --p-level 6 --o-collapsed-table genus-table.qza
qiime tools export --input-path genus-table.qza --output-path abs-table
biom convert -i abs-table/feature-table.biom -o "${location_path}Taxonomy_Classification/analysis/outputs/abs-genus-table.tsv" --to-tsv