I am a PhD student working on bacterial diversity of different Arctic ecosystems. I am in the learning phase of Qiime2. I could successfully do the data processing as per the instructions given in the qiime2 tutorials following Atacama and moving picture tutorials. I was trying to make the otu count table from the table.qza file using the commands mentioned in the forum: Exporting and modifying BIOM tables (e.g. adding taxonomy annotations).
I could successfully retrieve the count table but while trying to add the taxonomy information to the OTU count table, I was not able to get the result. I am still getting the same OTU count table without any taxonomy information.
Here are the commands that I have used:
qiime tools export --input-path table-nonchimeric-wo-borderline.qza --output-path exported_table-nc-wobl-new
biom head -i exported_table-nc-wobl-new/feature-table.tsv
qiime tools export --input-path nc-wobl-trained-taxonomy.qza --output-path exported_table-nc-wobl-new
cp exported_table-nc-wobl-new/taxonomy.tsv biom-new-taxonomy.tsv
the headers of biom-new-taxonomy.tsv was
Feature ID Taxon Confidence
This was changed to : #OTUID taxonomy confidence
saved and did the following steps.
biom add-metadata -i exported_table-nc-wobl-new/feature-table.biom -o table-with-taxonomy-nc-wobl-new.biom -m sample_metadata.tsv --observation-metadata-fp biom-new-taxonomy.tsv --sc-separated taxonomy --observation-header OTUID,taxonomy,confidence
biom convert -i table-with-taxonomy-nc-wobl-new.biom -o feature-table-nc-wobl-new-with-taxonomy.tsv -m sample_metadata.tsv --to-tsv
There is no error message generated. The command is getting executed but no taxonomy is added to the count table.
Can anyone suggest how to rectify this issue.