Using custom primers for a run requires two additional steps during run setup:
|•||Prepare and add the appropriate volume of each custom primer to the custom primer positions of the reagent cartridge.|
|•||Download and select the custom primer recipe during run setup.|
All other steps follow the run setup workflow. Refer to Protocol for sequencing protocol instructions.
When custom primers are used for Read 1 or Read 2, the software directs the instrument to pull from the CP1 and CP2 wells. Therefore, Illumina primers are not used for the sequencing run. Illumina primers refer to primers already in the reagent cartridge.
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.