Region in detail
Region in detail allows you to browse genes, variations, sequence conservation, and other annotation along the genome. There are three main panels (or images), shown in Figure 1.
FIGURE 1 - REGION IN DETAIL
The first panel (Chromosome Image) shows the chromosome of interest, marking any haplotypes or patches in red or green, respectively.
FIGURE 2 - (SCROLLABLE) OVERVIEW IMAGE
The next panel is called the Overview Image. It shows a 1 Mb overview of Ensembl and Havana genes along the chromosome (depicted as a blue bar). The individual contigs that make up the genomic assembly are coloured in light or dark blue.
Gene colours are as follows:
- Gold and red genes: protein coding
- Grey genes: pseudogenes
- Blue genes: non-coding
The overview image is scrollable in up to date versions of Chrome, Firefox, and Internet Explorer 9 and later. There is also support for Safari 5.1, but may not work on certain old Macbooks.
To scroll along the genome, click (and hold) the scroll arrows (A), or click and drag within the image.
Use the track height button (B) to switch between automatic track height (arrows facing in icon) and fixed track height (arrows facing out icon), and reset to default using the arrow wheel button. In the fixed track height mode, adjust the height by dragging up and down from the paired horizontal lines between the tracks. As you scroll across the chromosome in automatic track height, the track height automatically adjusts to fit in all features. In fixed track height, you may find that not all features within a track are displayed, and the height needs to be adjusted to fit them in.
Jump to a position in your display using the drag/select tool (C). Click the double ended arrow to select drag/select, the icon will change to a vertical dotted line. Drag a box in the image and select Jump to region. You can also drag and select a region by holding down the shift key as you select a box in the image.
In either the scollable or static display, icons are available to configure the page, share the view, resize the view, and export the image
FIGURE 3 - REGION IMAGE
The third, Region Image, allows a more zoomed-in view, and is further explored in Figure 3.
Data tracks (genes, cDNA alignments, etc.) are shown above and below the blue bar. Tracks above the blue bar are on the forward strand of the chromosome, and tracks under the blue bar are on the reverse strand. Reorder the tracks by using the vertical blue bar at the left. To zoom in or change the display, use our zoom slide, or enter in basepairs manually. Alternatively, click any gene or transcript and select the location to zoom in on the feature. The Move/Select option in the top right of the image allows you to choose your action on click and drag. Select Move to move along the genome with a click and drag, let go to allow the page to reload with your new location. Select Select to drag out a box around a region or feature of interest, use it as a marker in the view or click on the pop-up to zoom in.
The Region Image supports user tracks, which you can display using the Add your data button in the left hand menu.
FIGURE 4 - CONFIGURE THIS PAGE
Add or change data tracks using the configure this page tool button at the left of the page, the cog wheel icons in the images, or click on the track name itself. Add data by navigating to the Custom data tab in the configuration window and clicking on Add a custom track.
You can also attach your own data eg. BAM files by clicking the Add your data button (or Manage your data if you already have custom data added) and uploading or attaching a file, from the main view.
Some tracks can be displayed in different styles, however there is a limit on how much data can be displayed in certain styles. This FAQ explains the styles available and the amount of data that can be displayed.