Filtering Step in 18S rRNA Analysis – Excluding Bacteria

Technical Support
1

Hello!
I am conducting an 18S rRNA analysis to taxonomically identify populations of eukaryotic organisms, with a particular interest in the presence and relative abundance of free-living amoebae.

I am using the PR2 database because I initially used the Silva database, but the identification of Acanthamoeba was nonexistent.

I would like to know how I can perform the filtering step, excluding not only mitochondrial and chloroplast sequences but also bacteria.

I have tried the following command:

qiime taxa filter-table
--i-table table_FACSA_FLA_18S.qza
--i-taxonomy taxonomy_FACSA_FLA_18S_PR2_V5_Acanth.qza
--p-exclude :bacteria,:mito,:plas
--o-filtered-table filtered-table_FACSA_FLA_18S_PR2_V5_Acanth.qza


I have also tried other variations in the `--p-exclude` option, such as:

--p-exclude bacteria,:mito,:plas \
--p-exclude :bact,:mito,:plas \


But none of them seem to work.

How could I run this?

Thanks in advance, 

Carla
2

Hello!
Could you try to run the same command but with:

--p-exclude "Bacteria"

as a test and report here if the issue was solved?

Best,