Custom sequencing primers on the MiSeq

For reference, see the MiSeq System Custom Primers Guide.
Custom sequencing primer positions:
  • Custom Read 1 primer: position 18
  • Custom Index Read primer: position 19
  • Custom Read 2 primer: position 20
When adding custom primers to the custom primer wells, pipette 600 l of custom primer at 0.5 M into the designated well.
Can only one custom index primer be used?
  • Yes, only index 1 may be custom or standard. Index 2 is primed off the oligo flow cell lawn (see the Indexed Sequencing Guide).
Alternatively, custom primers can be spiked into the existing Illumina sequencing primers. For further information, search for Knowledge Base article Spiking custom primers into the Illumina sequencing primers.
For any feedback or questions regarding this article (Illumina Knowledge Article #2414), contact Illumina Technical Support [email protected].
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