Hi!
I am trying to use green genes 2 as my database for assigning 16s sequences. I saw that there is a greengenes reference alignment available in the SOP. Would this reference be sufficient for alignment and then I can use green genes 2 database for analysis?
I tried using green genes 2 as a reference for allignment and get this error:
mothur > align.seqs(fasta=CL1.trim.unique.fasta, reference=greengenes2.fasta
Reading in the greengenes2.fasta template sequences… [ERROR]: template is not aligned, aborting.
DONE.
It took 0 to read 0 sequences.