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,
You can filter your
FeatureData[Sequence] using the table produced by decontam, see this tutorial: https://docs.qiime2.org/2019.1/tutorials/filtering/. Once filtered, you can perform feature classification to generate taxonomy (see Moving Pictures tutorial).
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
–p-exclude mitochondria, chloroplast
Again, thanks a lot!
qiime feature-table filter-seqs \
--i-sequences rep-seqs.qza \
--i-table table_filtered_decontam.qza \
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