I am currently trying to analyse my ITS1 samples. AFAIK, ITS works differently as their region length is variable. Therefore, when I try to trim off the primer using
bbduk, I use the parameter below:
bbduk.sh in1=MSA_S21_L001_R1_001.fastq.gz in2=MSA_S21_L001_R2_001.fastq.gz \ out1=MSA_S21_L001_R1.fastq out2=MSA_S21_L001_R2.fastq \ ktrim=l k=22 mink=20 hdist=1 copyundefined=t ordered=t rcomp=t \ literal="GGAAGTAAAAGTCGTAACAAGG,GCTGCGTTCTTCATCGATGC" tpe tbo
I then use
DADA2 and noticed that most of the input is filtered out and I think this is due to the primer trimming.
Has anyone else did the same thing as me?