Need help to create a barplot of my data with the qiime taxa barplot visualizer.

[s_lang (Sebastian Lang)]

I have run the pipeline from @Deni_Ribicic q2ONT- q2 workflow for analysis of full length ONT 16S rRNA gene reads with my Nanopore data of a 16S sequencing. Importing the ONT data, training the classifier with the SILVA database and the rest of the pipeline worked well, the following data was generated from the basecalled data:
1_total_run.fastq.gz
2_demux-reads (folder)
3_QC (folder)
4_single-end-demux.qza
4_single_end-demux.qzv
5_derep-seqs.qza
5_derep-seqs.qzv
5_derep-table.qza
5_derep-table.qzv
6.1_uchime-ref-out (folder)
6.2_new-ref-seqs-op_ref-85.qza
6.2_rep-seqs-op_ref-85.qza
6.2_table-op_ref-85.qza
7_aligned-filtered_derep-seqs.qza
8_masked-aligned-filtered_derep-seqs.qza
9_unrooted-tree.qza
10_rooted-tree.qza
11_taxonomy-sklearn.qza

and exported:
dna-sequences.fasta
feature-table.biom
table-with-taxonomy.biom
taxonomy.tsv
tree.nwk

Now I want to create a barplot of the data with the qiime taxa barplot visualizer (https://docs.qiime2.org/2019.10/plugins/available/taxa/barplot/). I would use as input Artifact Table the file “6.2_table-op_ref-85.qza” and as input Artifact taxonomy the file “11_taxonomy-sklearn.qza”. Are these the correct files?
But I also need a metadata file. Can someone please tell me how to generate it from the above data.

I also uploaded the file “10_rooted-tree.qza” to iTol (https://itol.embl.de/) to visualize the results, but unfortunately the tool only shows the tree with the OTU-IDs and not with the taxa. Even if this is a qiime foreign tool, maybe somebody knows how I get the taxa here.

If you need more information please let me know.
Thanks a lot!

[Deni_Ribicic]

@s_lang

Now I want to create a barplot of the data with the qiime taxa barplot visualizer (barplot: Visualize taxonomy with an interactive bar plot — QIIME 2 2019.10.0 documentation). I would use as input Artifact Table the file “6.2_table-op_ref-85.qza” and as input Artifact taxonomy the file “11_taxonomy-sklearn.qza”. Are these the correct files?

Yes, those are correct ones!

But I also need a metadata file. Can someone please tell me how to generate it from the above data.

The metadata file should contain sample identifiers in the first column, named as #SampleID. Sample identifiers are the names of your samples, which should correspond to ONT barcodes, e.g. BC01, BC02, etc.. Then you can add more columns describing your samples = metadata.

I'd also suggest to explore @MaestSi nanopore 16S pipeline MetONTIIME, which is more flexible and up to date.

[s_lang (Sebastian Lang)]

@Deni_Ribicic
thank you very much for your quick and helpful answer. Creating the metadata file worked. I started with the example file from the Metadata Tutorial. Consequently, the creation of the barplots has now worked.

The correct display with iTol now also works. If you insert the files 10…, 11… and 6.2… according to the thread Loading Greengenes tree in iTOL it works.

[Deni_Ribicic]

Perfect! Glad it worked well.