# Get Regional Methylation

The Get Regional Methylation task uses a region annotation (.bed) file to generate regions from CpG methylation count data. For each region specified in the annotation file, methylation counts of all CpG sites within the region are averaged to produce a count value in a regions-by-samples count matrix.

## Using a built-in promoter regions file

A built-in annotation model based on human (hg38) promoter regions from ENSEMBL version 114 is provided. To invoke Get Regional Methylation task,

* Click on **5-base Methylation** data node.
* Select **Region analysis** from context-sensitive menu, select **Get Regional Methylation**.
* Select **Homo sapiens (human) - hg38** from **Assembly** and **Promoters Ensembl release 114** from **Annotation model** drop-down, then click **Finish**.
  * If you do not see 'Promoters Ensembl release 114' from the Annotation model drop-down, following these steps to add the built-in promoter regions annotation:
    * select **Add Annotation model** from **Annotation model** drop-down.
    * In **Add annotation file** dialog, select **Homo sapiens (human)** at *Species*, **hg38** at *Assembly*, **Promoters Ensembl release 114** at *Annotation model drop-down*, **Download annotation file** at *Creation options*, then click **Create**.

<figure><img src="/files/LP1VDm0j5fhnbqAVoQt0" alt=""><figcaption></figcaption></figure>

## Using a custom regions file

When you have a list of regions of interest, you may upload a custom region bed file for the Get Regional Methylation task. The custom regions file should:

* Consists of 3 columns: chromosome, start position, and stop position. The positions should be 0-based coordinates.
* No columns name.
* Tab-delimited.
* Saved as .bed file.

After the custom region file is prepared, following these steps to apply it on the Get Regional Methylation task:

* Click on **5-base Methylation** data node.
* Select **Region analysis** from context-sensitive menu, select **Get Regional Methylation**.
* Select an **Assembly**, and select **Add Annotation model** from **Annotation model** drop-down.
* In **Add annotation file** dialog, select **Add Annotation model** from **Annotation model** drop-down, type in a **name** for the custom annatation, select **Import annotation file**, then click **Create**.

<figure><img src="/files/o0JriejMFJ16mEGaYObD" alt=""><figcaption></figcaption></figure>

* At **Select file** page, select **My Computer.**
* Click **+ Choose** button to choose a .bed file from your computer.
* The selected file name will be displayed, click **Next**.

<figure><img src="/files/cAQF5ITqS58AkJBe1OCp" alt=""><figcaption></figcaption></figure>

* Select **Other** for **Annotation type,** click **Next.**
* Click **Finish** to run Get Regional Methylation based on the selected custom regions file.

<figure><img src="/files/BvlIyC8JjrvZ2c9qf6eb" alt=""><figcaption></figcaption></figure>


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