> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/design-studio-array/product-guides/assay-design/design-assay.md).

# Design the Assay

1. From the Microarray Designer toolbar, select **Start Design**.
2. \[Optional] To view a detailed comparison between the iSelect and XT iSelect assays, select **Compare Assays**.
   * This option is available if you have access to XT iSelect.
3. Select one of the following assay options:
   * **EX-24 iSelect / EX-24 iSelect +**
   * **EX-48 iSelect / EX-48 iSelect +**
   * **HTS iSelect / HTS iSelect+**
   * **XT iSelect / XT iSelect+ (Genotyping ONLY)**
   * **Commercial+**\
     Each assay option includes information on the minimum and maximum limits.
4. Select one of the following design options:
   * **Custom** — Create a fully custom design.
   * **Add on to Existing Design** — Add content to an existing custom design.
5. Enter a name for the design.
   * Invalid characters include: plus sign (+), ampersand (&), backslash (\\), slash (/), colon (:).
6. \[Optional] Enter a description for the design.
7. Select **Next**.
   * The Configure Design screen opens.
8. Select a species from the **Select your species** drop-down list, and then select **Add Species**.
   * You can select up to four species for XT iSelect.
9. Select **Next**.
   * The Upload Targets screen opens. Refer to [Input Target Files](/design-studio-array/product-guides/input-target-files.md) for information on input target files, including templates and settings.
10. From the **Select File Type** drop-down, select the file type you want to upload.
    * \[Optional] Select the **Lowercase Weighting** sequence file type option to weight the final score of lowercase nucleotides to reflect suboptimal probe placement for lowercase regions.
    * \[Optional] Select **Update Annotations** to display updated annotations (if available) for design targets in the resulting score file. This option only applies to existing design or score file types.
11. Select **Submit for Design**. When the design completes without errors, the software updates the session status and sends you an email notification. If the design fails, an error message appears with details of the issue. Refer to [Output Files](/design-studio-array/product-guides/output-files.md) for more information on errors.


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