Removing taxa from table not removing but moving to unassigned

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1

Hi,

I removed Eukaryota from my samples since I had a lot of host DNA. However, what happens is that when you make the taxa bar plot, you can see that those sequences were not removed and just moved to unassigned sequences. Otherwise, why wouldn’t the relative abundances change?

2

Hi @Negin,

How did you remove the Eukaryota? Could you walk me through the steps/commands?

Best,
Justine

3

Yes, here is the code I used:

Remove Euakaryota from the feature table

qiime taxa filter-table
–i-table /home/n-z/valizad2/dissertation_pilot/microbiome_analysis/Oct122018/dada2/v4_20181012/single/V4-20181012-table-dada2.qza
–i-taxonomy /home/n-z/valizad2/dissertation_pilot/microbiome_analysis/Oct122018/taxa/v4-20181012/silva-99-132/V4-20181012-taxonomy-99.qza
–p-exclude Eukaryota
–o-filtered-table /home/n-z/valizad2/dissertation_pilot/microbiome_analysis/Oct122018/dada2/v4_20181012/single/V4-20181012-table-no-Eukaryota.qza

Make taxa plot without the Eukaryota

qiime taxa barplot
–i-table /home/n-z/valizad2/dissertation_pilot/microbiome_analysis/Oct122018/dada2/v4_20181012/single/V4-20181012-table-no-Eukaryota.qza
–i-taxonomy /home/n-z/valizad2/dissertation_pilot/microbiome_analysis/Oct122018/taxa/v4-20181012/silva-99-132/V4-20181012-taxonomy-99.qza
–m-metadata-file /home/n-z/valizad2/dissertation_pilot/microbiome_analysis/Oct122018/metadata/v4/20181012-sample-metadata.tsv
–o-visualization /home/n-z/valizad2/dissertation_pilot/microbiome_analysis/Oct122018/taxa/v4-20181012/silva-99-132/V4-20181012-taxa-bar-plots-99-no-Eukaryota.qzv

4

Hi @Negin, it sounds like you were able to resolve your filtering issue on this other thread (linked below), but please let us know if you are still having issues related to filtering unclassified/eukarya.

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5

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