# Planning a Manual Mode Run on NovaSeq X/X Plus
**Background**
There are two options to setup a Manual Mode run on the NovaSeq X/X Plus.
1. Manual Mode (Generate BCLs Only): Select this option if not performing secondary analysis (FASTQ Generation). Can import a sample sheet with sample names and indexes.
2. Import sample sheet for local analysis (Manual Mode) - Select this option to import a v2 sample sheet and perform secondary analysis.
**Manual Mode Run Setup**
1. To sign into the Control Software, enter the username and password, and select Sign In.
2. Select **Start**.
3. Select **Sequencing**.
4. Select an instrument side to perform the run.
5. At the top of the runs list, select **Manual** to switch to manual run entry.
* Planned is the default run selection. To change the default setting, refer to '*Set Default Run selection*' section from [Customize System Settings](https://support-docs.illumina.com/IN/NovaSeqX/Content/IN/NovaSeqX/InstrumentCustomization.htm)
6. If performing a local secondary analysis:
* For Run Type, select **Import sample sheet for local analysis**.
* Select and open the sample sheet v2 file. For information on sample sheet v2 formatting and requirements, refer to the [Sample Sheet v2 Resource](https://help.connected.illumina.com/run-set-up/overview).
7. If not performing a local secondary analysis for the manual run:
* For Run Type, select **Manual run** (**generate BCLs only**).
* Enter the Run Name (The run name can contain a maximum of 225 alphanumeric characters, spaces, dashes, and underscores).
* Select single or paired-end for the read type.
* Enter the number of cycles performed in each read:
* Read 1 — Enter the cycles number.
* Index 1 — length of the index read for Index 1. For a PhiX-only run, enter 0 in both index fields.
* Index 2 — length of the index read for Index 2. For a PhiX-only run, enter 0 in both index fields.
* Read 2 — Enter the cycles number.
* \[Optional] Select the sample sheet. For information on sample sheet v2 formatting and requirements, refer to the [Sample Sheet v2 Resource](https://help.connected.illumina.com/run-set-up/overview).
8. Select **Review** to review the current run.
9. To use custom primers:
* For NovaSeq X Series Control Software v1.2.2 and earlier, download the appropriate custom primer recipe XML file from the [NovaSeq X Series Product Files](https://support.illumina.com/sequencing/sequencing_instruments/novaseq-x-novaseq-x-plus/product-files.html) on the Illumina support site.
* For NovaSeq X Series Control Software v1.3 and later, select the applicable custom primer checkboxes. Uploading a custom recipe disables the custom primer checkboxes.
* For more information on custom primers, refer to [Custom Primers](https://support-docs.illumina.com/IN/NovaSeqX/Content/IN/NovaSeqX/CustomPrimers.htm).
10. \[Optional] If the instrument is connected to the cloud, confirm the cloud run setting.
11. Confirm the output folder.
* For runs with cloud storage enabled, the following options are available:
* To transfer run data to a local storage folder in addition to the cloud, provide an output folder.
* To only transfer run data to the cloud, select **Don't transfer run data to external output folder.**
* To change the default output folder, refer to [Specify the Default Output Folder Location](https://support-docs.illumina.com/IN/NovaSeqX/Content/IN/NovaSeqX/SpecifyOutputFolder.htm).
12. If performing local secondary analysis, confirm BCL data folder transfer setting.
* To update the default run data management selection, refer to *'Set default Run Data management'* section from [Customize System Settings](https://support-docs.illumina.com/IN/NovaSeqX/Content/IN/NovaSeqX/InstrumentCustomization.htm).
13. \[Optional] Select a custom recipe file, refer to [NovaSeq X Series Product Files](https://support.illumina.com/sequencing/sequencing_instruments/novaseq-x-novaseq-x-plus/product-files.html)
* If using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit or the Illumina Stranded mRNA Prep kit, select the custom recipe required. See [Custom recipes for Illumina Stranded libraries on NovaSeq X/X Plus](https://knowledge.illumina.com/instrumentation/novaseq-x-x-plus/instrumentation-novaseq-x-x-plus-faq-list/000008394)
14. When finished, select **Load consumables**.
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| *For any feedback or questions regarding this article (Illumina Knowledge Article #8540), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000008540%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |
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