I believe this is what I need!
I need a table with taxonomy as rows, the samples as columns and the read counts as intersections. Can I get this with this tutorial Link BIOM table with taxonomy - #3 by Ghaz? Or to do this one I need a BIOM table first (no ideia how to use biom)?
This is what I have tried:
I ran qiime taxa barplot, which gave me a QZV of interactive barplots. From that, I downloaded a CSV with samples as rows and taxonomy as columns. I transposed that CSV using Pandas to change taxonomy into rows and samples into columns. It seemed to have worked out.
BUT the taxonomy is written in an ugly way, like this example:
k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__ovatus
Is there a way to make this more readable?
Do you have any thoughts on the way I did it?