Hi!
In the "Application" section of the README file, which explains how to generate the reference files of SILVA v138.2 (https://mothur.org/blog/2024/SILVA-v138_2-reference-files/#application), it says that the V4 region of the 16S rRNA gene can be obtained with the following commands:
mothur "#pcr.seqs(fasta=silva.nr_v138.align, start=11894, end=25319, keepdots=F, processors=8); unique.seqs()"
When I checked the binding position of the primers for the V4 region with ARB, I found that the start and end positions should be 11895 and 25318, respectively. Is there a reason why the parameters 11894 and 25319 are used, and could this be related to the bug in pcr.seqs() that was fixed in mothur version 1.47.0 ("Fixes bug with pcr.seqs If keepdots=f, and start and end are used, then first base was removed by mistake."; https://github.com/mothur/mothur/releases/tag/v.1.47.0)?
Thank you very much for your help!
Hi!
In the "Application" section of the README file, which explains how to generate the reference files of SILVA v138.2 (https://mothur.org/blog/2024/SILVA-v138_2-reference-files/#application), it says that the V4 region of the 16S rRNA gene can be obtained with the following commands:
mothur "#pcr.seqs(fasta=silva.nr_v138.align, start=11894, end=25319, keepdots=F, processors=8); unique.seqs()"When I checked the binding position of the primers for the V4 region with ARB, I found that the start and end positions should be 11895 and 25318, respectively. Is there a reason why the parameters 11894 and 25319 are used, and could this be related to the bug in pcr.seqs() that was fixed in mothur version 1.47.0 ("Fixes bug with pcr.seqs If keepdots=f, and start and end are used, then first base was removed by mistake."; https://github.com/mothur/mothur/releases/tag/v.1.47.0)?
Thank you very much for your help!