I read that ASVs are for 90nt, 100nt or 150nt and that the forward reads should be used and trimmed down to 150nt. I might be overthinking this and getting myself confused. This is the command I have used for DADA2 to truncate my sequences to 150nt.
Because this is just the forward read, should I be truncating at 150nt so I have bases 0 -150. Or should I be trimming the left and right end of the sequence so I have the sequence bases (70nt - 220nt).
The ASVs placed in Greengenes2 are derived from Qiita, where the standard processing only uses the forward read. The 150nt would be from the 3' end of the fwd primer (i.e., does not include the primer). Does that make sense?
If you want to compare data sets, processing all of them the same way is important!
Qiita uses Deblur with these settings (90, 100, 150) and other lengths like 200 and 250 too!
These are implemented in DADA2 as --p-trunc-len as they truncate (remove from the end) of the read.
DADA2 also addes the trim-left setting to trim from the very start of the read. Deblur does not have this.