After Filter with Negative Controls (Decontam)

[Manuela_Ramalho]

Congratulations on Qiime2! You are fantastic!
I'm new to Qiime 2 and I have some problems, can you help me?

I have filtered my negative controls using Decontam in R and I have already imported to Qiime2 my new table_without_contaminants.qza, But I can not generate taxa barplot.
I guess that's because one of the necessary arguments is taxonomy.qza, and this file I generated before filtering with Decontam. Anyone have any tips?

Also, I'm having trouble knowing the subsequent analysis after filtering with Decontam. Is there a tutorial (that include filter negative controls and next) or any other tips/ideia/suggestion?

Thanks in advance!

All the best,
Manu

[thermokarst]

You can filter your FeatureData[Sequence] using the table produced by decontam, see this tutorial: Filtering data — QIIME 2 2019.1.0 documentation. Once filtered, you can perform feature classification to generate taxonomy (see Moving Pictures tutorial).

[Manuela_Ramalho]

Thank you very much for helping me!
In that case, should I then put the filtered table of Decontam into "--p-include"? Like this?

qiime rate filter-seqs
--i-sequences rep-seqs.qza
--i-taxonomy taxonomy.qza
--p-include table_filtered_decontam.qza
--p-exclude mitochondria, chloroplast
--o-filtered-sequences sequences-filtered_decontam-no-mitochondria-no-chloroplast.qza

Again, thanks a lot!

[thermokarst]

Not quite:

qiime feature-table filter-seqs \
  --i-sequences rep-seqs.qza \
  --i-table table_filtered_decontam.qza \
  --o-filtered-sequences sequences-filtered_decontam-no-mitochondria-no-chloroplast.qza