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Does the MiSeq verify the number of cycles in a planned run with the cycles in the reagent kit?
For MiSeq Control Software v3.1 and below:
The MiSeq Control Software does not cross-reference the total number of cycles programmed in the run set up compared to the number of cycles a reagent kit can support. If a run is set up with a greater number of cycles than the reagent kit supports, the Control Software will still allow the run to proceed and run performance may be impacted. Runs may stop with Best Focus or Z-motor soft focus limit errors.
For MiSeq Control Software v4.0 and above:
With the introduction of MiSeq Control Software v4, the Software checks the total number of cycles and makes sure it is less than or equal to the total cycles supported by the loaded reagent kit. This will take into account the 7 dark cycles required for Index Read 2 if the workflow uses dual index sequencing.
If the planned cycles exceeds the supported cycles of the reagent kit, this error will present after pre-run checks complete and will show the following message:
If this error presents, review the cycle numbers for each read, and verify that the loaded kit supports the number of cycles required for desired workflow.
For more information on this topic, refer to the following Illumina Knowledge Articles