# How to use a 10X Multiome ATAC Library custom recipe for NextSeq 500/550 When sequencing 10X Multiome ATAC libraries on the NextSeq 500/550, a custom recipe is required to account for the 24 bp i5 index. This article shows how to install the custom recipe and how to set up runs using the custom recipe. For more information why a custom recipe is needed for 10X Multiome ATAC libraries, see this article on the 10X Genomics website: [Why do I need a custom recipe when sequencing Multiome ATAC libraries on the NextSeq 500/550?](https://kb.10xgenomics.com/s/article/360051084471-Why-do-I-need-a-custom-recipe-when-sequencing-Multiome-ATAC-libraries-on-the-NextSeq-500-550) To obtain the custom recipe, email and request a custom recipe for 10X Multiome ATAC libraries for NextSeq 500/550. Confirm which NextSeq 500/550 Control Software (NCS) version is installed on the instrument. From the NCS home screen, select **Manage Instrument** and then select **About** to determine the NCS version. After obtaining the custom recipe from Illumina Tech Support, add the custom recipe folders to the instrument. **Using the custom recipe with NCS v4** **Installing the custom recipe** 1. Unzip the custom recipe folders obtained from Illumina Technical Support. 2. Copy each unzipped folder to the appropriate location on the NextSeq 500/550. * The folder 'NSQ8DCI2v2.5\_MO' is the Mid Output folder, and must be placed in the 'Mid' folder, located here: * C:\Program Files\Illumina\NextSeq Control Software\Recipe\Custom\Mid * The folder 'NSQ8DCI2v2.5\_HO' is the High Output folder, and must be placed in the 'High' folder, located here: * C:\Program Files\Illumina\NextSeq Control Software\Recipe\Custom\High ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-fe3c908aeece5fb2f288db859d44c2f6b1cd297d%2Fimage4.png?alt=media) Figure 1: Folder structure for installing the custom recipe in NCS v4. **Setting up a run with the custom recipe in NCS v4** 1. Navigate to **Manage Instrument** from the home screen, select **System Customization**, select the **Enable Custom Recipes** checkbox, and select **Save**. 2. To use the custom recipe, the NextSeq 500/550 **must be run in standalone mode**. * Local Run Manager (LRM) and BaseSpace do not support custom recipes. 3. Run Setup. * Choose **Manual** as run mode; do not select BaseSpace for storage. * Under **Run Setup**, enter the desired read length (50 x 8 x 16 x 49). * Load the flow cell. * Load the buffer. * Load the reagents. * On the bottom right of the next window, locate the Recipe drop-down. It is set to 'High' by default. Select the drop-down then select the custom recipe for the sequencing kit (Figure 1). * Select **Next** and proceed with run set up as usual. ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-41c09cc9aa6bf0b6f716203492d66bea5cf3742f%2Fimage5.jpg?alt=media) Figure 2. Selecting a custom recipe in NCS v4 during run set up. After sequencing is complete, change all settings back to proceed with original standard run recipes. * Select **Manage Instrument** from the home screen, select **System Customization**, deselect the **Enable Custom Recipes** checkbox, and select **Save**. Standard recipes will be usable with this option disabled. **Using the custom recipe with NCS v2** **Installing the custom recipe** 1. Unzip the custom recipe folders obtained from Illumina Technical Support. 2. Copy each unzipped folder to the appropriate location on the NextSeq 500/550. * The folder 'NSQ8DCI2v2.5\_MO' is the Mid Output folder, and must be placed in the 'Mid' folder, located here: * C:\Illumina\NextSeq Control Software\Recipe\Custom\Mid * The folder 'NSQ8DCI2v2.5\_HO' is the High Output folder, and must be placed in the 'High' folder, located here: * C:\Illumina\NextSeq Control Software\Recipe\Custom\High **Setting up a run with the custom recipe in NCS v2** 1. Place instrument in standalone mode. * To use the custom recipe, the NextSeq 500/550 **must be run in standalone mode**. BaseSpace does not support custom recipes. 2. To put the instrument in standalone mode, select **Manage Instrument** from the home screen, select **System Configuration**. Select the **BaseSpace Configuration** option, then select **Standalone**. 3. Run Setup. * Under Run Set Up, enter the Run Name and Library ID. * Select the **Custom Recipe** from the Recipe drop-down (Figure 2). * Choose **Paired End** for the **Read Type**. * Enter the desired read length (50 x 8 x 16 x 49). * Select **Next** and proceed with run set up as usual. ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-50a908dc952964519033cb2c7a3dcaf017c899c5%2Fimage6.png?alt=media) Figure 3. Setting up a run with a custom recipe in NCS v2. After sequencing is complete, change all settings back to proceed with original standard run recipes. * Select **Manage Instrument** from the home screen, select **System Configuration**. Select the **BaseSpace Configuration** option, then select the **BaseSpace** option. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #7480), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007480%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |