We have to trim the sequence before denoising, for that, I am using the cutadapt tool.
We have used the 16S Metagenomic Sequencing Library Preparation for our samples, where we have used the V3-V4 region.
My first question is when I use the cutadapt, what part of the forward and reverse primer should I used for trimming.
should I use the this-
cutadapt -g CCTACGGGNGGCWGCAG -G GACTACHVGGGTATCTAATCC
or the entire sequence
cutadapt -g TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG -G GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC
Similarly, when we train the classifier, what part of the primer should I use for extracting the reads? Is it going to be the entire forward and reverse sequence?