# MiSeq: Run Set Up

## Configure Cloud Connectivity in MiSeq Control Software <a href="#e2euserguidedraftmiseq-configurecloudconnectivityinmiseqcontrolsoftware" id="e2euserguidedraftmiseq-configurecloudconnectivityinmiseqcontrolsoftware"></a>

1. From the **Main Menu**, select **System Settings**.
2. Select the **Run Settings** tab.
3. Select the **BaseSpace** tab.
4. *Optional*: Select **Turn on Illumina Proactive Support** to enable the Illumina Proactive monitoring service.
5. Select the region the instrument should connect to. This setting is used to ensure proper data storage is sent to Illumina Proactive Support and BaseSpace Sequence Hub.
6. *Optional:* Select **Private Domain** and enter the private domain of your Enterprise BaseSpace Sequence Hub account, if applicable.

## Set Up Sequencing Run with Cloud Analysis Sample Sheet <a href="#e2euserguidedraftmiseq-setupsequencingrunwithcloudanalysissamplesheet" id="e2euserguidedraftmiseq-setupsequencingrunwithcloudanalysissamplesheet"></a>

1. From the Home screen, select **Sequence**.
2. From the Run Setup Option screen, select **Manual**.
3. From the BaseSpace Options screen, select **Use BaseSpace™ Sequencing Hub for this run**.
   1. Select the **Run analysis, collaboration, and storage** option to send all run data to BaseSpace Sequence Hub.
   2. Enter your BaseSpace Sequence Hub account credentials.
   3. Select **Sign In**.
   4. Select the Workgroup.
4. Select **Next**.
5. Set the Read Type, Read Length and Custom Primers for all of your cycles.
6. Browse to select your sample sheet file. See [here](https://help.connected.illumina.com/overview/auto-launch-settings#e2euserguidedraftmiseq-userunplanningtoexportasamplesheet) for information on how to download a sample sheet file.
7. Select Next.
8. Continue to set up the sequencing run as per the [MiSeq System Product Documentation](https://support.illumina.com/downloads/miseq-product-documentation.html).


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