I’m working on a dataset of 2 x 300 bp obtained by Illumina MiSeq, and I’m now looking at the quality bar-plots, obtained after demultiplexing.
I was trying to figure out the best parameters for denoising (in particular, trimming length).
I calculated a 52 nt overlap ( lenght of the amplified region - median forward length - median reverse length).
( I amplified the V3 - V4 region)
So: 550 - 301 - 301 = - 52
According to this result, how many bp have to be trimmed (from 3’) in order to perform dada2 trimming? (parameters --p-trim-left-f and --p-trim-left-r)
I assumed them to be both 26 (?).
Thank you in advance!