Redoing bar plots

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

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

Hi Colin,

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

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?

The main outputs are these:


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

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

Thank you for your patience.

That's the output of qiime taxa filter-seqs and qiime taxa filter-table, see: ampliseq/modules/local/ 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!

Let us know what you try next!

Hi Colin,

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

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