Hey Pat,
While giving the command for pcr.seqs, the main prompt of the website shows that silva.bacteria.fasta should be used as reference (when V4 region was in question), but I visited the ‘blog post’, in which the silva.seed_v123.align (when V3 region was in question) file was used for the pcr step, which one is accurate and why?
You can see the pictures acquired from the mothur site below,
