I followed the mothur Miseq SOP using my raw data from Novaseq. From my understanding, the raw data should contain adapter, but I just followed the whole SOP without removing adapter, still got the final taxanomy file. Is my result reliable? or maybe does it prove that there’s no adapter or primer in my raw data?
Hi - have you looked at the sequences to see if you can find the adapters/barcodes/primers? I’d be surprised if you see the actual adapters. The way we sequence generates the barcode sequences separately and the machine uses those to demultiplex the sequences. Because we use the primers to sequence the barcodes and the 16S region we don’t generate sequence data with primers.