I used DESeq2 to see which ASVs were differentially abundant on 16S metabarcoding data. I now want to plot the relative abundance (in %) of those ASVs.
However, I am unsure which data to plot: is it ok to simply use the raw read table (transformed to %) or should I use a normalized or transformed reads count table (rlog or vst)? Wouldn't the second option be less true to the original data?
I am sorry as this is probably a very basic question, I just can't figure it out!
Thank you very much :)