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?
Hi Yergaliyev
Thanks for the help. I did use the merge command and it went smoothly. I used the command like this:
qiime feature-table merge
–i-tables feature_table.qza
–i-tables feature_table2.qza
–o-merged-table merged_table.qza
Also summarise the merged table with this command:
qiime feature-table summarize
–i-table merged_table.qza
–o-visualization merged_table.qzv
–m-sample-metadata-file sample-metadata-16S.tsv
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?
Hi
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
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:
Output
(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: