Obtaining sequences per biological sample

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Hi @rnasrah,

I'm just a user and not on the developing team but here's my first attempt to contribute a little to this forum!

I recently asked about some additional sorting options regarding the rep-seqs visualization table, and it looks like it is something the team might develop in the future. See that post here. I thought it might be relevant to your question. If not...

Depending on what you are looking for exactly, here are a couple of options easily available:

  1. If you are just looking for a quick visualization of your samples' content the taxa barplot output gives a nice visual where you can look at the composition of each of your samples at various levels, plus it has some nice additional sorting options. There's also download tabs on the upper-left hand side of this output that allows you to download a .csv version of the data. In the official moving pictures tutorials, this is the taxa-bar-plots.qzv barplot which comes following taxonomic assignment so if you wanted to look at the content prior to this step see option 2.

  2. If you are looking for the true sequence variants (prior to taxonomic assignments) then you can retrieve that by exporting (or simply unzipping using your own preferred tool) the denoised feature table. In the moving pictures tutorial this would be the table-dada2.qza . Within it there is a .biom table under the data folder which will have the sequence variance x sample table. This will look like the former OTU tables except instead of the taxonomy or OTU# it will have the unique SV ID, ex: d1df10ad656760686c75a3884fa9fc2d
    In this option you will have to find an appropriate way to read or convert the .biom file as its not your typical text file.

Hope this helps!

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