Split MiSeq run into 16S and ITS

Commands in mothur
1

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.

2

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

3

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