> 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/dragen-stratamap/illumina-connected-multiomics/data-input.md).

# Data Input

The analysis results from the DRAGEN Spatial Transcriptome software can be loaded into Illumina Connected Multiomics (ICM) for investigation and additional analysis. This page will cover how to manage studies in ICM. For more information on the general platform, see the [Illumina Connected Multiomics User Guide](https://help.multiomics.illumina.com/icm).

[Navigating to ICM](#navigating-to-icm)

[Creating a new study](#creating-a-new-study)

[Adding data to a study](#adding-data-to-a-study)

[Deleting a study](#deleting-a-study)

## Navigating to ICM

There are multiple ways to get to the ICM platform:

* Go to ICM directly with the following path: <https://use1.icm.illumina.com/icm/>
* Go through the Illumina platform page and select "Illumina Connected Multiomics" <https://platform.login.illumina.com/platform-home>
* Go through ICA by clicking the icon with a nine dot grid pattern at the top right and selecting "Illumina Connected Multiomics" <https://ica.illumina.com/ica/>

Through each of those pages, log in with valid credentials, and select the desired domain.

ICM opens to the "Studies" page.

## Creating a New study

To make a new study:

1. Click "+ New Study" in the top right.
2. Enter a study name and description.
3. Select "I want to choose my preferred ICA project" and then select the ICA project you would like to pull data from. You can select it from the existing project dropdown list.
4. Click "Create".

<figure><img src="/files/AlNs3FBXVDgKzPNwkCUR" alt=""><figcaption></figcaption></figure>

### Adding Data to a Study

There are two ways in which your data can be added to ICM: Manual Ingestion or Autoingestion.

Both methods will add the sample data to the Data tab and allow you to start a new analysis, if desired. After an analysis is manually started, the analysis results will be viewable in the Overview or Analyses tab of a Study.

### Manual Ingestion (Recommended)

To manually add data per sample to a study:

1. Open your desired study.
2. Click "+ Add Data" at the top left of your study page and then "Select from ICA project": 1.

   ```
   <figure><img src="../.gitbook/assets/image (10).png" alt=""><figcaption></figcaption></figure>
   ```
3. Select "Spatial" from the data type dropdown menu and then also select "Spatial Transcriptomics": 1.

   ```
   <figure><img src="../.gitbook/assets/image (11).png" alt=""><figcaption></figcaption></figure>
   ```
4. Next, select the "Illumina Spatial Solution" format: 1.

   ```
   <figure><img src="../.gitbook/assets/image (12).png" alt=""><figcaption></figcaption></figure>
   ```
5. Select the box that says "Show manifest files".
6. Navigate to the desired analysis folder and select the "results" folder.
   1. For data from a BSSH managed and initiated run, the analysis folder will be in the "ilmn-analyses" folder. Select the run name that does not have "ws\_" appended to the start. Select the "results" folder.
   2. If the data was transferred to ICA through other means, navigate to the location used. Select the "results" folder.
7. Within the "results" folder, select the sample folder you would like to analyze.
8. Check the box next to the samples "pipeline-manifest.json" file: 1.

   ```
   <figure><img src="../.gitbook/assets/image (13).png" alt=""><figcaption></figcaption></figure>
   ```
9. Click "Add selected data to your study".
10. The data will then be available within the Data tab of your study homepage.
11. To manually create and initiate a sample analysis with this data, proceed to the "Spatial Analysis" section of this guide.

{% hint style="danger" %}
If your manually ingested sample analysis status displays "Error" in red or remains stuck as "Pending" for more than an hour, please refer to the "Abort and Retry Sample Analysis" subsection below for guidance on how to proceed.
{% endhint %}

### Autoingest

Within the settings of a study homepage ("Gear" icon at the top right), an "Update study" pop-up will appear and there will be an option to "Automatically import data from pipelines".

This will enable the Autoingest feature for **all samples** from the existing ICA project selected.

* **It is not recommended to check this box:**

<figure><img src="/files/wIsNzgUHVnYURafPRVE1" alt=""><figcaption></figcaption></figure>

{% hint style="danger" %}
If you choose to check this box and your autoingested sample analysis status displays "Error" in red or remains stuck "Pending" for more than an hour, please refer to the "Abort and Retry Sample Analysis" subsection below for guidance on how to proceed.
{% endhint %}

### Abort and Retry Sample Analysis <a href="#deleting-a-study" id="deleting-a-study"></a>

If a sample analysis status remains stuck as "In Progress" or "Pending" or "Error", the analysis may need to be aborted and retried.

{% hint style="info" %}
If this "Abort and Retry Method" doesn't fix the issue, please contact Illumina Support.
{% endhint %}

To abort and retry a sample analysis:

1. Within a study, navigate to the Analyses tab.
2. Select the list view icon at the top right.
3. Find your "stuck" analysis in the list and choose the Abort icon.

<figure><img src="/files/VePoYYRJCWhPspFgh4JT" alt=""><figcaption></figcaption></figure>

4. The page will automatically refresh and then you will see and select the Retry icon.

<figure><img src="/files/d1Q8wfnZjzysqCXNr21D" alt=""><figcaption></figcaption></figure>

5. The page will automatically refresh again and the analysis will restart.

## Deleting a Study <a href="#deleting-a-study" id="deleting-a-study"></a>

To delete a study:

1. Navigate to the Studies page from the left side menu.
2. Navigate to list view with the icon at the top right.
3. Click the trash icon associated with the study.

<figure><img src="/files/ZRtBK85OC5bUUXzdpUS9" alt=""><figcaption></figcaption></figure>

\\


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