How to get rid of Archaea spp. in my dataset

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1

Hello,

I am using https://cancer.usegalaxy.org/ to analyse a dataset containing the bacterial 16S V4 region in some environmental sample. My taxonomy assigned OTU table has some archaea. How can I get rid of the Archaea species before rarefying my data?

I tried to manually remove the Archaea spp. from the excel sheet and converted the excel's file format from xlxs to BIOM.
Then I uploaded the data to galaxy and used QIIME 2 tools import to import the data as featuretable [Frequency] in BIOMV210 format but the qza file I got could be be used to plot an alpha rarefaction curve.

How can I address this issue?

Thank you in Advance,
Brigitta

2

Hello!
Yes, it is possible within qiime2. ("d__" part can be different depending on the database):

    #if you want to keep only bacteria 
    qiime taxa filter-table \
        --i-table table.qza \
        --i-taxonomy taxa.qza \
        --p-include d__Bacteria \
        --o-filtered-table bact-table.qza
    
    #if you want to exclude certain domain
    qiime taxa filter-table \
        --i-table table.qza \
        --i-taxonomy taxa.qza \
        --p-exclude d__Archaea \
        --o-filtered-table no-arch-table.qza
5 Likes
3

HI @timanix ,

It worked! Thank you