Is there a way when viewing the “reps-seqs.qzv” file to divide up the number of a given sequence (feature) on a per sample basis? I’d really like to be able to generate a box plot for each sequence, but simply knowing how many samples contain a given feature would be useful. It’s helpful in thinking about whether or not some very abundance sequence was distributed broadly among samples or if it’s really just in a handful of samples. That matters when you’re trying to track cases of sequence index bleed.
One workaround is to use
qiime tools export to export your feature table into a .biom file. Then you can use the biom-format software to run
biom summarize-table --qualitative --observations on your .biom file to see how many samples each feature is observed in. You will already have the biom-format software installed in your QIIME 2 conda environment, so no need to install anything extra!