Split MiSeq run into 16S and ITS

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

O. A.

You’ll want to separate those at the very beginning, like in the make.contigs step.

Pat, how do i do that? any guidance will be great. (can mothur do it, or just rely on R or linux)