Congratulations on finishing your analysis, @lilycrook!
@vheidrich’s answer covers your questions pretty well - I just have a couple more breadcrumbs for you. Because most people only use the DADA2 denoising stats for diagnostic work (rather than publications), there aren’t links at this time to export most of the tables in that visualization.
To get the denoising stats data without a lot of copy-pasting, you can use
qiime tools export. This will, by default, export a .tsv. E.g.
qiime tools export \
--input-path my_dada2_stats_file.qza \
There are a couple ways you could tackle getting the per-sample frequencies from your table. If you need a programmatic solution, there are directions in other forum posts on how to export your feature table and make it into a .tsv. You’ll still have to do some work with the table to sum the frequencies across features. Python, R, whatever will do this for you in a reproducible way.
If you don’t need a programmatic approach, you can just copy-paste the Sample and Feature Count columns from the interactive sample detail page into a spreadsheet - that could be your already-exported dada2-stats, or a new .tsv. If you like excel, you can use an
if formula to match sample ids. If you go this route, be careful that your sample-ids are always stored as plain text. If you paste them into a number-formatted column in excel, leading zeros will be dropped and your sample-ids may not match each other or the rest of your data.