Question on: Customize your reference alignment for your favorite region

[zoha234]

hello, i am new to this field and just starting learning mothur, i have querry that i have sequence that i have to align with only v4 region from silva database and i have silva.bacteria.batabase. how do i extract v4 region from that silva database in mothur. as i don,t know about primers, how could i know about primers as well?

[pschloss]

If you're using the V4 region, then you can follow the instructions directly from the MiSeq SOP