I’m new to Mothur.
I’ve finished Miseq SOP tutorial based on mothur.org
Because of curiosity, I ran the analysis using tutorial fastq files with Silva 138.1 (mothur-compatible).
Compared to tutorial, it gave me different results. Of course I expected it, but I have few concerns.
Those are my questions.
(1) In tutorial, silva aligned database was used for align.seqs and RDP database was used for classify.seqs. Why? Why different database in single analysis?
(2) Hence, I re-analysed tutorial files using Silva 138.1 for both align.seqs and classify.seqs. It worked perfectly. But, gave me different results. I understand differences but it was too different. Was this coming from different database for classify.seqs between tutorial and re-analysed myself? I just wonder if I analyze my own data, should I use silva 138.1 for align.seqs and RDP 18 for classify.seqs? or It is OK to use silva 138.1 for both align.seqs and classify.seqs?
Below are two results. For example, (1) the most abundant phylum is Bacteroidetes in tutorial, but Bacteroidota in reanalyzed. (2) TM7 and Tenericutes are founded in tutorial version, but none in silva 138.1. (3) Patescibacteria is founded in silva 138.1 version, but not in tutorial version. Which one should I trust?
[this is used tutorial database (silva for align.seqs and RDP for classify.seqs]
[ this is used whole database (silva 138.1 for align.seqs and classify.seqs]