Removal of singletons: feature-table-filter not working

Hi again,

I have a quick question, I almost forgot to look at the singletons in my table, and after looking over the file I realized that there are quite a few singletons present. Fungal-table-dada2.qzv (574.3 KB) . I attempted to filter them out using the following code:

Filter out singletons (Only 1 present)

*qiime feature-table filter-features *
--i-table Fungal-table-dada2.qza
--p-min-frequency 2
--o-filtered-table Fungal-table-dada2-ns.qza

#Verify removal of singletons and choose rarefaction depth
qiime feature-table summarize **
--i-table Fungal-table-dada2-ns.qza **
--o-visualization Fungal-table-dada2-ns.qzv **
--m-sample-metadata-file Metadata-Fungal.tsv
Fungal-table-dada2-ns.qzv (578.4 KB)

After comparing the files to see if the singletons were removed, I see that they in fact where not. I have used this code before, on a different dataset, and I was able to removes this time. I'm really unsure what of what I am doing wrong, and have looked at other post, and my code seems to be fine.

Any ideas?

Hi @fabipc!
Based on the qzv you shared, it appears to be removing all features that appear only once. The bottom of the middle column shows that the smallest feature frequency is 2, as expected. (Sorry about the little stagger in these screenshots.)



Maybe I'm misunderstanding what you're trying to filter out?
Let me know,


Hi Chris,

All I have to say is wow!! :open_mouth: I definitely should not be doing bioinformatics at 1am. I was looking at the number of samples instead of the frequency and could not understand why the code I had used before was not working this time.

Thanks, and sorry for the “dumb” question. :smiley:


We’ve all been there, @fabipc! Glad everything’s OK after all. :wink:

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