I created my custom silva.v4.fasta from silva.full_v123.fasta instead of silva.bacteria.fasta mentioned in MiSeq SOP.
I made silva.full_v123.fasta by following instructions provided in:
This is because I wanted to include both Archaea as well as Bacteria.
I just wanted to make sure I am on the right track because we have to analyse some environmental samples – that can include diverse organisms. Is my approach correct?
=== Question 2
By the way, similar to MiSeq SOP (an excellent resource) for mapping taxonomy from 16S data for bacteria and archaea, do we have a similar resource for 18S taxonomy analysis.
This is because in our project we wanted to identify all components of an environmental sample like:
bacteria, fungi, algae, protozoa,…
Please suggest. Thank you in advance.