How can I found out what percentage of my sequences were classified on a per sample basis if all of my samples were imported as one Qiime artifact? If it is highly variable I will need to control for that when comparing relative abundances. I used open-reference clustering method. Thanks!
I am assuming that you have a feature table and taxonomy classification results. You can use
qiime taxa barplot to build a barplot, which will show the % of unassigned in each sample.
If you want a tabular output instead, you can use
qiime taxa collapse to collapse your feature table’s features based on taxonomic affiliation, use
qiime feature-table relative-frequency to convert to relative frequency, and then use
qiime tools export to export to biom,
biom convert --to-tsv to convert to text, and then examine that table directly.
I hope that helps!
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