The exon-only view "virtual chromosome" is constructed of all the exons present in the gene track specified in the multi-region configuration window. Exon "slices" are visually separated by blocks of intronic or intergenic bases, the size of which are set by the padding field. This designates the padding on both sides of an exon, and therefore is additive, e.g., a padding size of 6 will result in a 12-base space between exon slices:
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 information. +
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+The gene-only view displays the bases and annotations that fall within the coordinates of a gene, but hides all of the intergenic bases except those used for padding (Example 2). As with exon-only mode, the padding field sets the number of intergenic bases displayed to visually separate each gene slice.
Because genes and alternate transcripts often overlap by a few bases, the windows created by the gene-only (and exon-only) mode may sometimes merge together. Reducing the number of padding bases may increase the number of alternate regions by allowing less intergenic space between genes. However, this overlap is a common feature for most of the Genome Browser gene sets, and should be no cause for concern.
@@ -208,46 +212,53 @@ will display a message asking if you would like to return to a default view at that location. If you prefer to return to your custom region instead, click . Otherwise, click "here" to return to the default view.
If the term is not found at all in the assembly, an error message will display.
When scrolling or zooming while viewing regions from a custom BED URL, the range is restricted to the BED-defined regions. Although you can still zoom in to single base resolution, the outward zoom is limited to the extent of the defined regions. Scrolling upstream and downstream is also limited to the BED-defined range.
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An additional viewing mode is available on human assemblies hg17 and later: showing an alternative
haplotype placed in its chromosomal context (Example 5). The haplotype is
specified by entering its ID in the form chr_name_alt in the configuration window. To view
the list of haplotype IDs for a given assembly, go to
http://hgdownload.soe.ucsc.edu/goldenPath/$db/bigZips/$db
.chrom.sizes,
where $db is the human assembly name (e.g., hg38, hg19, hg18 or
hg17).
Alternatively, haplotypes can be viewed using the Alt Map... track in the Mapping and Sequencing group. Open the track and navigate to the haplotype of interest in the track window. Click on the haplotype to display its details page, then click the link Show this alternate haplotype placed on its chromosome.
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