Hi, I am rerunning the mothur miseq SOP and noticed that the new SILVA file is called “silva.nr_v138_2.align” and not silva.bacteria.fasta like the one in the SOP. I have never used a reference database before and have only ever copied the mothur sop to a tee, so I am wondering where this fits in the sop instructions? Is this the same file as the silva.bacteria.fasta file?
Hi there - yep, this is effectively the same as silva.bacteria.fasta except that it also includes archaea and eukarya. You should use silva.nr_v138_2.align or any of the other version where you would have used silva.bacteria.fasta
Pat
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