miki
November 16, 2021, 10:36am
#1
I want remove "d__Bacteria" in texa bar plot.
However I can not remove it.
Now I can remove Unassigned only.
I wright my command below.
qiime taxa filter-table
--i-table table.qza
--i-taxonomy taxonomy.qza
--p-exclude “Unassigned, d__Bacteria;”
--p-mode exact
--o-filtered-table remove.qza
qiime taxa barplot
--i-table remove.qza
--i-taxonomy taxonomy.qza
--m-metadata-file metadata.tsv
--o-visualization remove.qzv
This commnad is not working.
timanix
(Timur Yergaliyev)
November 16, 2021, 10:42am
#2
Hello and welcome to the forum!
Hope, you don't mind that I removed duplicated topics.
Regarding your issue, could you try:
qiime taxa filter-table
--i-table table.qza
--i-taxonomy taxonomy.qza
--p-include “p__”
--o-filtered-table filtered.qza
By providing --p-include “p__” plugin will remove any sequence that was not assigned to the phylum level, so unassigned and assigned only to "Bacteria" features will be removed
5 Likes
system
(system)
closed
December 17, 2021, 4:43pm
#3
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