I am following the MiSeq SOP and have not been able to figure out how to find the SILVA alignment positions for our particular primers (515F and 806R) needed for the pcr.seqs command. I also tried the oligos parameter as a work around, which fails when I try to run align.seqs. I’ve been through SILVA and mothur a number of times and haven’t been able to find this information or instructions on how to get it. I apologize if I missed it. Thanks for your help.
What version of mothur are you using? We corrected a bug with the removing of primers in pcr.seqs that was causing the template to be unaligned for the align.seqs command. http://www.mothur.org/wiki/Mothur_v.1.31.0#Bug_fixes