Hello everybody,
This is my first post as I am new in the forum and using Qiime2 as well.
I am working with sequences of 16S obtained from an Illumina Miseq.
I have 7 samples with 5 replicates each (so 35 paired-end samples). I have managed to obtain the taxonomic box plots (as you can see in the screenshot) of the samples separately but I don’t know how to use the information of my 5 replicates together. Thank you in advance for your help! 
Replicates management
Hi! You can group your table before plotting so each column will represent a mean or median value for the group
https://docs.qiime2.org/2019.7/plugins/available/feature-table/group/
4 Likes
Hi! Thank you for your answer!
I still can not make it work… Which feature table should I use as imput?
I have done first this:
qiime dada2 denoise-paired --i-demultiplexed-seqs /home/demux-paired-end.qza --p-trunc-len-f 0 --p-trunc-len-r 0 --p-trunc-q 20 --output-dir /home/OUTPUT
qiime feature-classifier classify-sklearn --i-classifier gg-13-8-99-nb-classifier.qza --i-reads /home/OUTPUT/representative_sequences.qza --o-classification taxonomy.qza
qiime metadata tabulate --m-input-file /home/taxonomy.qza --o-visualization /home/OUTPUT/taxonomy_full.qzv
qiime taxa barplot --i-table /home/OUTPUT/table.qza --i-taxonomy /home/taxonomy.qza --m-metadata-file /home/metadata.tsv.csv --o-visualization /home/OUTPUT/+taxa-bar-plots_full.qzv
And then as you suggest, before the barplot comand this:
qiime feature-table group --i-table /home/OUTPUT/taxonomy.qza --p-axis sample --m-metadata-file /home/OUTPUT/metadata.tsv.csv --m-metadata-column Group --p-mode ‘mean-ceiling’ --o-grouped-table grouped_rep_seq.qza
But it does not work…
Thanks in advance.
HI again
As an input you should provide table.qza
As an output - grouped-table.qza
And then to use grouped table as an input for taxabarplot command.
Also the extension of your Metadata file looks strange, it should be metadata.tsv without .csv at the end
