Can secondary analysis run on MiSeq while a run is in progress?
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It is not possible to perform secondary analysis on the MiSeq when a sequencing run is in progress.
If a new sequencing run is started on the MiSeq before the secondary analysis of a previous run is complete, the secondary analysis is stopped automatically.
MiSeq computing resources are dedicated to either sequencing or analysis, and the system is designed in such a way that a sequencing command overrides an analysis command.
Secondary analysis can later be requeued from the MiSeq Reporter or Local Run Manager Analyses tab, when sequencing is not in progress.
For any feedback or questions regarding this article (Illumina Knowledge Article #2604), contact Illumina Technical Support .