sliva bacteria region position

Theory behind mothur
1

Hi All,

I am just curious to know if I am using silva bacteria aligned database as my reference database, from which position to which position is the region for, say V1-V3, or V3-V6, etc. I know the total column length is 50,000. But do we have something posted somewhere to make sure I get the right region?

Say from position 1 to 13500 is v1to v3, from 13500 to 26900 is v3-v5? Do we have an arbitrary cutoff for that?

Thank you,

huaiying

2

Everyone’s primers differ a little so I’m very hesitant to put up hard numbers like this. Here’s what you need to do…

  1. Run pcr.seqs on silva.bacteria.fasta with your oligos file including the forward and reverse primers, set keepdots=T
  2. Run summary.seqs on the output and look at the start and end columns - these are the numbers you’ll want for your region of interest.