# Run Mode options for the MiSeq i100 Series

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-d392b937636758ad8ff8e41936df17c4a186dca7%2Fimage1.png?alt=media)

**Cloud (BaseSpace Sequencing Hub Setup and Analysis)**

* Use Run Planning setup in BaseSpace Sequencing Hub.
* Secondary Analysis takes place in Cloud.

**Hybrid (BaseSpace Sequencing Hub Setup and Local Analysis)**

* Use Run Planning setup in BaseSpace Sequencing Hub.
* Secondary Analysis performed using Local DRAGEN.

**Local (Local Run and Local Analysis)**

* Runs created through either instrument Control Software or through Illumina Run Manager.
* Secondary Analysis performed using Local DRAGEN.

**Sample sheet (Run Setup through importing Sample sheet)**

* Can import Sample Sheet (v2) either through Local Run Planning options or via Manual Mode tab.
  * Control Software v1.1 updated Run Setup workflow to separate selections between Planned Runs, Sample Sheet Import, and BCLs Only.
* Secondary Analysis is performed using Local DRAGEN Analysis only
  * Cloud Analysis is not allowed for Sample Sheet workflow.
  * Cloud Settings can be configured to upload FASTQ and BAM/CRAM files for data storage and sharing through BaseSpace if desired.

**Manual Mode**

* Run setup using Manual Mode Tab (for BCLs only).
* Sample Sheet can be attached (but will not be validated and not used for local analysis), no FASTQs generated.

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #9218), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009218%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |