Custom Primers

Illumina primers are in positions 12, 13, and 14 of the MiSeq reagent cartridge.

Reservoir	Read
12	Read 1 Primer Mix
13	Index Primer Mix
14	Read 2 Primer Mix

You can use custom sequencing primers for a run on the MiSeq. To do so, specify the use of custom primers in the sample sheet, and then load prepared custom primers into the empty reservoirs on the MiSeq reagent cartridge. The empty reservoirs are labeled 18, 19, and 20, and each reservoir is associated with a specific read in a sequencing run.

Reservoir	Read
18	Read 1 custom primer
19	Index Read custom primer
20	Read 2 custom primer

You can use a combination of custom primers and standard Illumina primers provided in the reagent cartridge. For example, you can use the Illumina primer for Read 1, a custom primer for the Index Read, and the Illumina primer for Read 2.