Hi all, apologies if this has already been asked here before, but why is the Mothur-formated SILVA database provided with the aligned sequences, while the RDP just has the unaligned sequences? I haven’t seen anything in the manual about recommended ways of generating an RDP alignment. Any insight would be helpful!
Thanks in advance!
The RDP alignment is pretty awful - they don’t try to align the variable regions. It’s not appropriate for alignments. The only reference alignment we encourage people to use is the SILVA reference. That being said, depending on your question, RDP, Silva, and greenegenes all have references that would be good for classification.
Pat
Hi both, sorry to jump in.
@pschloss I am wondering: what if I would like to use RDP database following the classic MiSeq SOP?
Because if I run pcr.seqs with the RDP reference files available here (RDP reference files), I obtain [ERROR]: seqs are not aligned. When using start and end your sequences must be aligned, and if I try to skip it, and go to align.seqs, turns out [ERROR]: template is not aligned, aborting.
Thanks in advance
Can you post your question to a new thread with the commands you are running? This thread is 6+ years old
Pat