Has anyone ever used multiple custom primers (read 1 primer, read 2 primer, and index primer) for amplicon sequencing?
We would like to try to combine 16S custom barcoded amplicon primers with ITS custom barcoded amplicon primers into 1 run. The amplicon sizes are pretty similar, so my only concern is with spiking the MiSeq V2 kit cartridge wells with multiple custom primers. If anyone has experience or insight on this it would be greatly appreciated!
Hi lauren,
you have two choices, mixing all primers in the same design and doing one library, or running both design to produce two librairies you'll mixed afterward (with different barecodes??).
I would prefer mixing all primers and run the multiplex, to avoid some bias, but only if all amplicons are targeting the same sample.
fred
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