v3 and v4 region on Silvia and GreenGenes database.

Commands in mothur
1

I don’t know if my question is “commands in mothur” related or not. I apologise in advance if it is not.
If I understoon correctly, “start” and “end” position in the “pcr.seqs” command provide starting and end position to trim the reference to make downstream analysis faster. my question is what are these positions for V3 and V4 region on both Silvia and GreenGenes database.


Thank you
2
  1. Find an Ecoli 16S sequence
  2. Trim the sequence to the region within your primers. Whether or not to keep the primer sequences doesn’t matter
  3. Align the trimmed sequence to the reference alignment (SILVA is preferred)
  4. Run summary.seqs on the aligned sequence
  5. Use the start and end numbers in pcr.seqs.