Removing singletons

Hey there,

Is there a way to remove singletons from feature tables?

Thanks!
–Lorinda

Hi @Lorinda,
Yes! You are looking for feature-table filter-features.

You would do something like:

qiime feature-table filter-features \
  --i-table table.qza \
  --p-min-frequency 2 \
  --o-filtered-table feature-frequency-filtered-table.qza

I hope that helps!

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@Nicholas_Bokulich Yes thank you! I guess I probably should have been able to find this on my own… Thanks for your time :slight_smile:

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Wouldn’t you have to set the min-frequency to 2 in order to remove all features with only 1 read?

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Thanks @Stream_biofilm for catching this! You are correct — I have edited the original post.

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I had that problem too! :roll_eyes:

Eventually I found this page listing all the qiime 2 'scripts’
https://docs.qiime2.org/2017.11/plugins/available/

I hope that help,
Colin

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