Hi mothur team,
I am processing 16S V4 data (515F/806R, ~253 bp reads). I want to customize the full-length latest SILVA v138.2 reference database to create a streamlined V4-only reference file.
What are the recommended exact start and end coordinates to use in pcr.seqs for the SILVA v138.2 database?
Thanks for help,
Richa
Hey there - You can find how I created the v138.2 reference files for mothur here: README for the SILVA v138.2 reference files
The start and end positions for V4 should be the same as what we use in the MiSeq SOP
Pat
Thank you Dr. Schloss. This is very helpful. I am following Miseq SOP and I am having trying to work with the seq.error step. I have zymo standard and I am trying to understand what do I have to do once I download the zymobiomics standard ref sequences. Is there any tutiral or page explaining this ? Thanks
You’ll need to generate a fasta file that contains the sequences in the mock community. The mock community fasta file does not need to be aligned. With that file and your data you should be good to go to follow this:
Pat