Filtering features frequency per sample (instead of across samples

I would like to do the following:
filter out features that are in counts of 10 or less IN a sample and not sure how to do it.

If I run the following command (see below), it will filter out features that are less than 10 counts ACROSS samples. But what I want is to filter out features that are less than 10 counts PER sample. Any ideas of how to do that?

qiime feature-table filter-features
–i-table table.qza
–p-min-frequency 10
–o-filtered-table feature-frequency-filtered-table.qza

  • I am using version Qiime2-2020.2, through conda.

Thank you so much!

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Hi @rnasrah,
Great question. This is unfortunately not possible within QIIME 2 yet, however there is an open issue on this request which means it may be added in a future version.

In the meantime you’ll have to export your table outside of QIIME 2 for this type of filtering (ex with R, or Python),


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