Demo - Exploring a genomic region in Pig

Demo: Exploring a genomic region in Pig

Searching for a region

Start at the Ensembl homepage, www.ensembl.org. In the species-specific search box, select Pig from the drop-down menu, enter 15:81890000-82000000 into the search box and click on Go. The format of your coordinates should be:
chromosome:start-end
You do not need to remove commas if there are any.

Press Enter or click Go to jump directly to the Region in detail page in Pig.

Region in detail

Click on the questionmark button button to view page-specific help. The help pages provide descriptions, labelled images and, in some cases, help videos to exaplin what you can see on the page and how to interact with it.

The Region in detail page is made up of three images, let’s look at each one in detail.  

Chromosome overview

The first image shows the chromosome overview:

You can jump to or highlight a different region by dragging out a box in the image using your cursor. Click and drag a box on the chromosome. A pop-up menu will appear.

If you want to move to the region, you can click on Jump to region (### bp). If you want to highlight it, click on Mark region (###bp). For now, we’ll close the pop-up by clicking on the X on the corner.  

Region overview

The second image shows a 1Mb region overview around our region of interest, which is marked in a red border. This view allows you to scroll back and forth along the chromosome.

You can also drag out and jump to or mark a region.

Click on the X to close the pop-up menu.

Click on the Drag/Select button to change the action of your mouse click. Click on the arrows to scroll along the chromosome by clicking and dragging your cursor within the region overview image. As you do this you’ll see the image below grey out and two blue buttons appear. Clicking on Update this image would jump the lower image to the region you scrolled to. We want to go back to where we started, so we’ll click on Reset scrollable image.

Region in detail view

The third image is a detailed, configurable view of the region.

Click on the Drag/Select option at the top right-hand corner to switch mouse action. Similarly to the region overview, you can select Drag, to scroll along the genome (the page will reload when you drop the mouse button). On Select you can drag out a box to highlight or zoom in on a region of interest.

Set your cursor action to Select, drag out a box around an exon and select Mark region.

The highlight will remain in place if you zoom in and out or move around the region. This allows you to keep track of regions or features of interest.  
 
 

Configuring the region view

We can edit what we see on this page by clicking on the blue Configure this page menu at the left.

This will open a menu that allows you to change the image.

You can put some tracks on in different styles; more details are in this FAQ: http://www.ensembl.org/Help/Faq?id=335.

Let’s add some tracks to this image. Add the All variants on genotyping chips - short variants (SNPs and indels) track in the pop-up menu. You can use the search bar to filter for the track, or you can select the track in the left-hand menu under Variation > Arrays and other. To enable the track, click on the square next to the track name and select the track style Normal.

Now click on the check icon in the top right-hand corner to save and close the menu. Alternatively, click anywhere outside of the pop-up menu. Wait for the Region in detail view to load. Once loaded, you should be able to see the track in the image. If the track does not appear in the image, no track features are present in your region of interest. You may need to scroll along the genome or zoom out to visualise a broader region.

We can also change the way the tracks appear by hovering over the track name then the cog wheel to open a menu. We can move tracks around by clicking and dragging on the bar to the left of the track name.

Sharing and exporting

Now that you’ve got the region view how you want it, you might like to show something you’ve found to a colleague or collaborator. Click on the Share this page button (either in the left-hand panel or at the top of the Region in detail view) to generate a URL. You can share the URL with your colleague, so that they can see the same view as you (including all the tracks and configurations you’ve added). The URL contains the Ensembl release number, so if a new release or even assembly comes out, your link will just take you to the archive site for the release it was made on.

You can also export the region image by clicking on the Export image button at the top of the Region in detail view, or export the data (i.e. the sequence or the annotation) by clicking on the Export data button in the left-hand panel.

To return this to the default view, go to click on Reset configuration at the top of the Region in detail view.