RDP database from official website result unaligned

Commands in mothur
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Hi everyone!
I am posting this to get support about the use of RDP. I am in fact running a mothur pipeline following MiSeq SOP, but instead of using Silva when I get to pcr.seqs, I would like to use RDP database. I retrieve it from the official page in mothur webisite, but mothur gives me an error message saying sequences are not aligned. How should I solve the problem to reach the end of my pipeline?
Thanks in advance!

Note: I am working with Mothur version 1.48 used in a singularity container found on docker, at link Docker and perfectly functioning with other databases.

Hey @pschloss I created a new thread as I was commenting an older one, like from 8 years ago. Hope this can stand better. Thanks!

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The RDP alignment is not aligned. You would need to align the RDP reference set to the SILVA alignment. You might align the RDP or greengenes databses against SILVA and then use pcr.seqs to select out a subregion for classification, but I really can’t think of a reason why one would want to align amplicon sequences to anything but the SILVA reference alignment. You might want to check out the following papers…

Pat

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