Trim silva.bacteria.fasta to V3-V4 region

Theory behind mothur
1

Hi guys,
Which start and end point should I use to trim the reference to V3-V4 region? Is there a map table or something?
I’v tried to use pcr.seqs with V3-V4 primers but failed due to the gaps.
Or maybe I can remove all the gaps, trim it to V3-V4 region, and align it to something to get the gaps back?
Thanks.

2

May be you are looking for this…
http://mothur.ltcmp.net/t/pcr-seqs-start-stop-for-v3-5-on-miseq/1608/2

3

Thanks, it’s helpful.