Multi Region Display Help
Introduction
The multi-region display allows users the ability to "slice" up their normal track viewing experience into a variety of different modes: exon, gene, or user defined BED coordinates, and visualize the track annotations only in those regions, effectively removing the intergenic, intron or otherwise unwanted regions from the viewing window.
In addition, for the human assemblies hg17, hg18, hg19 and hg38, the multi-region view also supports embedding a haplotype chromosome on top of it's reference sequence in order to visualize the differences between the haplotype sequence and the reference sequence.
Using the multi-region display, one can:
- Show all the SNP's that are within exons using the exon only view.
- Show only the genes on a chromosome with the gene only view.
- Display the same chromosomal position on either side of a gene in order to model a repeat region using a BED file with custom regions.
- See how an alternate haplotype fits onto it's chromosome with the alternate haplotype view.
Getting Started with the multi-region view
Use the following instructions to display mutliple regions in the genome browser.
Step 1. Pick a genome assembly and region
- Select the genome assembly you would like to view just as when normally viewing an assembly, by using the top menu's Genomes link. If you would like to view custom regions for your assembly hub, navigate to it's browser display as normal.
- Once an assembly has been selected, you may search for a gene of interest or select a region to view using the Genome Browser search bar if desired, just as normal.
Step 2. Select the multi-region view
- Click while on the default display
page to bring up the multi-region configuration window:
Step 3. Configure the multi-region view
- By default the Show single-chromosome view will be selected. This
is the standard Genome Browser display, and can be used to return to a
standard display.
- Now we can select which multi-region view we would like to display:
- For exons only select Show exons
- For genes only select genes using ...
- For custom regions select Custom regions from BED URL
- For a haplotype chromosome select Show one alternate haplotype...
- Select the Highlight alternating regions in multi-region view box if you would like every other "slice"to be highlighted in blue.
- Now we can select which multi-region view we would like to display:
- Click submit to be taken back to the Genome Browser display:

An example exon only view.
After entering multi-region mode, the usual browser display configurations will still work, such as zooming in and out, reversing and resizing the view, highlighting and zooming to the highlighted selection, and track search.
Searching and zooming
Searching and zooming while using custom BED regions are a little different than while in
exon or gene only and haplotype mode. Searching should work normally when in gene only,
exon only, and haplotype mode, however in custom regions mode, the process is slightly
different, see the About Custom Regions section for more
information.
Additionally, while viewing custom regions, the browser can only zoom out as far as the BED defined coordinates, although single base resolution is still available. Again, for more information see the About Custom Regions section.
About the multi-region modes
Exon Only Mode
The exon only view removes any bases that fall within an intron from the display, thus
removing those annotations as well. Intergenic sequence is also removed, resulting in a
browser display consisting of annotations and bases that only fall within an exon or
padding region.
The exon only view is built by gathering all the exons present in the gene track listed next to the genes using option in the multi-track configuration window, adding the appropriate number of intron or intergenic bases specified by the padding field, and building a "virtual" chromosome. These form the slices of the exon only mode.
Visual spacing between exons is controlled by the padding field. The number of bases pads each side of an exon, in effect doubling the number of padded bases specified, as shown below, where padding is specified as 6:
If the gene track used to compute the slicing is a super track or contains other transcripts, only the longest exon will be used to determine slicing, regardless of whether or not they are in the same transcript. See Example 1 for more infromation.
Gene Only Mode
The gene only view is similiar to the exon only view, however it removes all
intergenic bases in a given range, thus only displaying annotations that fall within the
coordinates of a gene.
As with exon only mode, gene only mode uses the padding field to set the number of intergenic bases to buffer each gene. On tightly packed chromosomes or regions where there is little intergenic space, be careful the padding is not set too high, or multiple genes may display as a single gene, since overlapping transcripts are considered as one region.
For an example of how both overlapping transcripts and intergenic padding affects the gene only view, see Example 2.
Custom Regions
The custom regions from BED URL mode allows the browser to display only those coordinates specified in a BED file, and thus allows for user-specific modeling of various regions.
Like BED custom tracks, some comments are supported in the BED files used by multi-region mode. The supported comments are:
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To use one of these comments, just include the comment at the top of your BED file, preceded by a "#", like so:
#database hg38 #shortDesc Example of a short description chr1 pos1 pos2 chr2 pos1 pos2
It is important to note that the BED files supported can be of any type, although only information from BED 3 or BED 12 files are relevant to the display. Be careful about the order of the regions specified, as the "slices" displayed are in order of the BED file, and not in order of their genomic position. Check out Example 3 for an illustrative example of how important this ordering is.
Searching and zooming while using custom BED regions are a little different than while in exon or gene only and haplotype mode. Searching should work normally when in gene only, exon only, and haplotype mode, however in custom regions mode, when a term or position is entered into the search box from the track display page, the browser first searches for the term within the multi-region view, and, if found, the browser will zoom to that feature.
If the term is not found in the BED defined regions but is found elsewhere, this message will ask if you would like to return to a default view at that location. Click ok to return to your custom region. |
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If the term is not found at all in our databases, then the normal search error message will trigger.
As mentioned in the Getting Started section, searching, scrolling and zooming while viewing regions from a custom BED URL may be a little counterintuitive. While viewing multiple custom regions, your view is limited to only the regions you have specified, so although you can still zoom in down to single base resolution you can only zoom out as far as the BED defined regions, and the up and downstream scrolling is also limited to the range specified in the BED file.
Haplotype
The human hg38, hg19, hg18 and hg17 assemblies all possess an extra feature while using the multi-region view: showing one alternative haplotype on it's chromosome.
#### How to structure the bigZips link to make this text work? ####
For a list of possible haplotypes, check the goldenPath/hg$/bigZips/hg$.chrom.sizes file,
where hg$ is one of either hg38, hg19, hg18 or hg17. Any haplotype of the form
chr_name_alt can be placed on it's chromosome, unlike the random and unplaced
sequences, which are currently not supported by the multi-region view.
For an example of how what the haplotype mode looks like in the browser, see example 5 below.
Examples
Exon only example
The below screenshot
shows the exon only view for the SOD1 gene in human assembly hg38. The 3rd "exon"
from the left falls within the intron of the actual SOD1 gene, but is shown as an exon
because it is part of the GENCODE v22 super-track.
Here is the hg38 mitochondrial chromosome, shown in gene only mode with padding set to 10:
Even though many genes are present on this chromosome, they are almost all overlapping with each other, preventing the gene only view from definining separate regions.
Now compare to the hg38 mitochondrial chromosome with padding set to 0:
With more alternating regions, we can see that not all the genes overlapped with each other, they simply had no intergenic space betweem them with which to draw slices.
Custom Regions example
Here is an example BED file for
mm10 that contains a list of exon positions for the Pax9 gene. If you load this file as
a custom track without turning on multi-region, you will notice that the blocks
display in order of genomic position, not in the order they are specified in the file:
However, if after loading the custom track you turn on multi-region mode and use the file as a list of custom regions, you will see that now all of a sudden the blocks are out of order, and the corresponding exons of the Pax9 gene have been split up and are out of order as well. This is a feature of the custom regions view, as it allows for display of previously difficult to model regions, such as centromeres or display or the same gene twice to compare annotations.
BED12 example
The following example BED file
utilizes a BED12 file to show two regions from two different chromosomes, chromosome
22 and chromosome 21, highlighting the human genes POTEH, CECR2, USP25 and CHODL.
chr22 15690026 17558149 chr22 960 + 15690026 17558149 0 2 31497,81057, 0,1787066 chr21 15730025 18267373 chr21 960 + 15730025 18267373 0 2 148887,22540, 0,2514808

The multi-region display utilizes the data in the blockStarts and blockSizes fields of the BED file in order to draw it's regions, allowing for even more customization of the genome browser display.
This example shows how the human hg38 haplotype chr1_KI270762v1_alt fits onto chromosome 1.
Not how annotations do not extend into or out of the haplotype region, since haplotypes are annotated separately from regular chromosomes.