pcr.seqs command

Commands in mothur
1

Hi,

I had some samples that were taken from the human gut. I am now trying to run the mothur pipeline for the microbiome analysis of the data. For the command, pcr.seqs, how do I know the start and end positions for the alignment? Also, is the silva database the only database available?

thanks!

2

or the command, pcr.seqs, how do I know the start and end positions for the alignment?

This is a question we seem to answer a lot…
http://mothur.ltcmp.net/t/pcr-seqs-start-stop-for-v3-5-on-miseq/1608/2

Also, is the silva database the only database available?

Although we only suggest using the SILVA reference alignment, other references are here:

For classification the references are here: