Hello everyone, i had the results of a MiSeq run (96 samples) where i ran 2 genes per sample. Each fastq that i received of the 192 fastq files contains both 16S and ITS. I ran make.contigs and it generated the fasta, … ect, so far. How can i separate the 16S and ITS based on F and R amplification primers? Ideally, at what stage those should be separated.
many many thanks