Custom Primers
Custom primers are not supported in Index First workflow
| • | Prepare and add the appropriate volume of each custom primer, or custom primer mix, to the custom primer well on the dry cartridge. |
| • | Configure the options in the |
All other steps follow the run setup workflow. Refer to Set Up a Run for Custom Primers, and then proceed to Protocol for sequencing protocol instructions.
Custom Primers and PhiX
When custom primers are used for Read 1 or Read 2, the software directs the instrument to pull from the respective custom primer well. Therefore, Illumina primers are not used for the sequencing run.
If Illumina primers are not used for Read 1 or Read 2, the optional Illumina PhiX control is not sequenced. To use the PhiX control with custom primers, contact Illumina Technical Support for guidance.
Because PhiX is not indexed, sequencing data from the PhiX control is not generated for index reads regardless of which indexing primer is used.
Primer Positions on the Dry Cartridge
You can use a combination of Illumina primers and custom primers in the same run. Depending on the combination specified, the software pulls the primer from the appropriate reservoir. For example, if a custom primer is used for Read 2 but not Read 1, the software pulls the Read 1 primer from the Illumina primer well and the Read 2 primer from the custom primer well.
