qiime taxa filter-table removing wrong taxa

User Support
1

Hello,

I'm trying to filter my feature table based on a taxonomic list of desired bugs (taxa_to_keep_donors.txt (1.3 KB)).

I broke it down into two steps, first:
Include generally everything I want (but there were a few taxa left to remove):

qiime taxa filter-table \
--i-table ../../filtered_table_min2samp.qza \
--i-taxonomy ../../taxonomy_silva138-99.qzv.qza \
--p-include Rothia,Bacteroidales,Streptococcus,Ruminiclostridium,ventriosum_group,xylanophilum_group,Butyrivibrio,Lachnospiraceae_UCG-006,UCG_003,incertae_Sedis,Negativibacillus,Anaerovoracaceae,Proteus,Oscillospiraceae \
--o-filtered-table filtered_all_taxa_to_keep.qza

This provided a table that I expected (after collapsing, converting to relative frequency, exporting, and converting to txt)
rel_freq_keep_L6.txt (56.6 KB)
I then went to exclude the extra taxa:

qiime taxa filter-table \
--i-table filtered_all_taxa_to_keep.qza \
--i-taxonomy ../../taxonomy_silva138-99.qzv.qza \
--p-exclude uncultured,UCG-005,DTU014,Colidextribacter,intestinimonas,NK4A214,Oscillibacter,Papillibacter,Pseudoflavonifractor \
--o-filtered-table filtered_lefse_taxa_temp.qza

This step is, unfortunately, removing taxa that don't match the exclusion terms (as far as I can tell).
rel_freq_lefse_taxa_L6_temp.txt (24.9 KB)

Taxa removed that I don't think meet the exclusion criteria:

d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotellaceae_NK3B31_group
d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotellaceae_UCG-001
d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridia;f__Hungateiclostridiaceae;g__Ruminiclostridium
d__Bacteria;p__Firmicutes;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio
d__Bacteria;p__Firmicutes;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Oscillospira
d__Bacteria;p__Firmicutes;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UCG-003
d__Bacteria;p__Firmicutes;c__Clostridia;o__Peptostreptococcales-Tissierellales;f__Anaerovoracaceae;g__Anaerovorax
d__Bacteria;p__Firmicutes;c__Clostridia;o__Peptostreptococcales-Tissierellales;f__Anaerovoracaceae;g__Family_XIII_UCG-001

I did a search on the first filtering table and each of the exclusion words only showed up once, so I'm not sure why the other taxa are being excluded.

What am I doing wrong in the exclusion step that these extra taxa are being removed?

Thanks!
Samantha

2

Hello!
I am totally not sure in my answer, and I do not know if it will work or not, but could you try to provide each of your patterns in ""?

4

Hi Timur,

Unfortunately, adding quotes around each pattern did not solve the issue. The table looks the same as the one posted before.

qiime taxa filter-table \
--i-table filtered_all_taxa_to_keep.qza \
--i-taxonomy ../../taxonomy_silva138-99.qzv.qza \
--p-exclude "uncultured","UCG-005","DTU014","Colidextribacter","intestinimonas","NK4A214","
Oscillibacter","Papillibacter","Pseudoflavonifractor" \
--o-filtered-table filtered_lefse_taxa_temp_v2.qza

~Samantha

5

That's a mystery to me.
But, is it possible that all errorously filtered taxa in your taxonomy file contain one of the patterns at level 7? For example, "uncultured".

6

You are right, the missing taxa had "uncultured" at level 7. I was able to fix this by excluding g__uncultured instead of just uncultured.

Thanks for your help!
~Samantha

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7

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