What will happen if I don't run the pcr.seqs command on Mothur?

I know my sample contains the V3-V4 region of the 16s rRNA but I don’t know it’s start and end. Would there be a problem if I skipped the pcr.seqs command and directly align my sequences on the entire gg/silva .refalign file?

That would be fine or you could consult this blog post on customizing your start/end positions for your region.


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