I am following mothur’s SOP pipeline for MiSeq (2x250bp) (used mothur’s latest version 1.48) but running the following command my sequences are reduced from 4 million to 1 million. I have many doubts to choose the maximum length since the amplicon obtained is in the V3-V4 region of the 16S that has a size of approximately 461bp, I have considered approximately maxlength = 480bp and here I have that very high reduction.
screen.seqs(fasta=stability.trim.contigs.fasta, count=stability.contigs.count_table, maxambig=0, maxlength=480, maxhomop=8)
Maybe someone could guide me or explain why this is due and if maybe I’m doing something wrong so I can correct it?
At the moment I don’t have the log file but I leave some screenshots
This first image is when make the contigs