Redoing bar plots

User Support
1

Hi there,

I have processed a number of samples (n= 30) which include negative controls and have produced a number of plots (alpha, beta, barplots). Is there a way to now remove the taxa found in the negative controls and re run the plots? I initially ran this in the nfcore/ampliseq pipeline. I have the rel-table-ASV_with-DADA2-tax file (which i manually removed the neg control hits) and wanted to know if there was a relatively straightforward way to redo the plots with this file and not say excel/pandas etc - If this file is what was actually used to generate these plots?

Many thanks

2

While we don't officially support nfcore/ampliseq, I bet we could help you do this within QIime2!

Does this pipeline give you any .qza files already in the Qiime2 format?

Also, a quick warning

A safer option may be this plugin: quality-control — QIIME 2 2023.5.1 documentation

3

Hi Colin,

Many thanks for your response. Yes aware of the cross contam issue as well! It does indeed give you .qza files

4

It does indeed give you .qza files

Can you post a list of all those files, then we will pick out one as a starting place?

5

The main outputs are these:

rep-seqs.qza
table.qza
taxonomy.qza

Others:
filtered-sequences.qza
abundance tables: filtered-table.qza, feature-table.biom

It's a shame the pipeline doesn't incorporate decontam-remove / identify etc.

6

Thank you for your patience.

That's the output of qiime taxa filter-seqs and qiime taxa filter-table, see: ampliseq/modules/local/qiime2_filtertaxa.nf at master · nf-core/ampliseq · GitHub

If you use the exclude_taxa setting, those taxa will be removed from this table.

Those two files are already in the correct format for quality-control and other plugins!
filtered-sequences.qza
filtered-table.qza

Let us know what you try next!

7

Hi Colin,

Many thanks, appreciate your response and will definitely give it a try!

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