# Run Mode options for the MiSeq i100 Series

![](/files/FcKxq3NWC3uwOw39OZUb)

**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.

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                        |
| :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *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)*.* |


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://knowledge.illumina.com/instrumentation/miseq-i100-series/instrumentation-miseq-i100-series-reference_material-list/000009218.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.