I will like to know how to join two biome table on qiime2.
I have two reads that I used in the qiime2 workflow and I need to join the two reads together before export to R for onward analysis.
Is there any tutorial to help or any workflow description?
Thank you for your help.
Here is the link to the feature-table related plugins that allow you to merge feature tables (bioms) and other artifacts:
This one is for feature tables:
After joining your tables, you can export it as a biom file.
qiime tools export \
--input-path merged_feature_table.qza \
Thanks for the help. I did use the merge command and it went smoothly. I used the command like this:
qiime feature-table merge
Also summarise the merged table with this command:
qiime feature-table summarize
Although, I have to merge the metadata tables too. I removed the ‘Sample ID’ header tag for the second table and validate the metadata table on Keemei.
The question is do I merge the taxonomy file and other files too that I need to export to R?
You can do it by the first link in my previous post.
Merge-seqs for representative sequences and merge-taxa for taxonomy.
Thanks a bunch for the lead. I was able to join the artifacts. I used these command lines:
For representative sequences -
qiime feature-table merge-seqs --i-data featureData_rep-seqs.qza --i-data featureData_rep-seqs2.qza --o-merged-data merged_featureData_rep-seqs.qza
For taxonomy file -
qiime feature-table merge-taxa --i-data featureData_taxonomy.qza --i-data featureData_taxonomy2.qza --o-merged-data merged_featureData_taxonomy.qza
But I am unable to visualize these artifacts. The visualization command reply that there’s no plugin for the visualisation of the files.
This is the command that I used and the output:
qiime feature-table summarize \
(1/1) Invalid value for ‘–i-table’: Expected an artifact of at least type
FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]. An artifact
of type FeatureData[Taxonomy] was provided.
Also, I tried to join the rooted-tree artifact. This is the command that I used and the output:
qiime feature-table merge-rooted-tree --i-data featureData_rooted-tree.qza --i-data featureData_rooted-tree2.qza --o-merged-data merged_featureData_rooted-tree.qza
Error: QIIME 2 plugin ‘feature-table’ has no action ‘merge-rooted-tree’.
Any advice or leads.
You are using a command for visualization of feature-table, providing a taxonomy file.
You need to use this one to tabulate taxonomy file.
I am afraid, the best strategy will be to construct a new tree using merged artifacts.
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