# Creating a list of regions

In this tutorial, the experimental goal is to identify regions with copy number changes in multiple patients. To do this, we will create a list containing deleted and amplified regions across the genome shared by 8 or more samples.

* Select **Create Region List** from the *Copy Number Analysis* section of the *Copy Number* workflow
* Select **Specify New Criteria**

We want to include all the amplified regions across the genome shared by at least 8 samples in our first criteria (Figure 1).

* Set *Name* to **Amplified**
* Set *Spreadsheet* to **2/segmentation/summary (segment-analysis)**
* Set *Column* to **6. Total Amplifications** using the drop-down menu
* Deselect the box next to *Include values less than or equal to*
* Set *Include values greater than or equal to* value to **8**

The *# pass* should be 86, indicating that 86 regions meet the criteria.

* Select **OK**

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-5b99cf414b59525a26d831307bc8a2d14e04331d%2Fimage2017-11-20%2013_12_39.png?alt=media)

Figure 1. Configuring the Amplified criteria

* Select **Save** to save the list
* Select **OK** to confirm that you would like to save *Amplified* as a list
* Select **Close** to exit the *List Creator* dialog

*Amplified* is now open in the *Analysis* tab as a child spreadsheet of *segmentation*. Although this list contains regions amplified in 8 or more samples, some samples may also contain deletions in the same regions. For downstream analysis, we may want to filter out these regions to create a final list with only amplified regions. Here, we will use the interactive filter.

* Select the *Amplified* spreadsheet
* Select ![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-e4f60a668e48b82a66db47d4cd0d2f700b3a6258%2Fimage2017-11-20%2012_46_58.png?alt=media) to open the interactive filter
* Set the *Column* drop-down list to **8. Total Deletions**
* Type **0** in the *Max* box
* Select **Enter** on your keyboard

This will apply a filter excluding any region with deletions (Figure 2).

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-c8f1ad50abd15d35483c72e6596282b448bb2047%2Fimage2017-11-20%2013_13_5.png?alt=media)

Figure 2. Interactive filter excluding regions with deletions.

The yellow and black bar on the right-hand side of the spreadsheet indicates the porportion of rows that have been filtered. Next, we can save the filtered list.

* Right-click the *Amplified* spreadsheet in the spreadsheet trees
* Select **Clone...** from the pop-up menu
* Set the *Name of the new spreadsheet* to **amplified\_only**
* Set *Create new spreadsheet as a child of spreadsheet* to **2/segmentation (segmentation.txt)**
* Select **OK**

The new spreadsheet is a temporary file. To keep the spreadsheet, we need to save it.

* Select *amplified\_only* in the spreadsheet tree
* Select ![alt text](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-745449868a6951e5cbd330d115bbe94495c63e37%2Fimage2017-9-26%2013_31_19.png?alt=media)
* Set the file name as **a\*\*\*\*mplified\_only**
* Select **Save**

The *amplified\_only* spreadsheet contains 60 rows and includes regions that were amplified in 8 or more samples and not deleted in any sample.

To create a list of regions only deleted in 8 or more samples, repeat the above steps for deleted regions. You should create a final list, *deleted\_only*, with 92 regions.

Next, we can merge the two lists to create a spreadsheet with both deleted and amplified regions.

* Select **File** from the main taskbar
* Select **Merge Spreadsheets...**
* Select the **Append Rows** tab
* Select \*\*2/segmentation/\*\***deleted\_only (deleted\_only)** from the *First Spreadsheet* drop-down menu
* Select **2/segmentation/amplified\_only (amplified\_only)** from the *Second Spreadsheet* drop-down menu
* Name the merged spreadsheet **amplified\_or\_deleted** using the *Specify Output File* (Figure 3)
* Select **OK**

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-c6003598af14ea1392be8071fc65b12e0f6e852a%2Fimage2017-11-20%2013_41_17.png?alt=media)

Figure 3. Merging amplified and deleted spreadsheets

* Select the new spreadsheet, **amplified\_or\_deleted** in the spreadsheet tree
* Select ![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-745449868a6951e5cbd330d115bbe94495c63e37%2Fimage2017-9-26%2013_31_19.png?alt=media) to save the spreadsheet

This spreadsheet, *amplified\_or\_deleted*, will be used as the basis for the downstream steps in this analysis.

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