In this example, you will create a custom track for a hic file that is already on a public internet server — data from an in situ Hi-C experiment on the HMEC cell line mapped to the hg19 assembly (Rao et al., 2014).
The line breaks inserted in the track line for readability must be removed before submitting this entry as a Custom Track. Click here for a text version you can paste without editing. The "browser" line above is used set the default view to a region of chromosome 21.
browser position chr21:32,000,000-35,000,000
track type=hic name="hic Example One" description="hic Ex. 1: in situ Hi-C on HMEC"
db=hg19 visibility=dense
- bigDataUrl=http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/hic/GSE63525_HMEC_combined.hicPaste the "browser" line and "track" line into the custom track management page for the human assembly hg19 (Feb. 2009), then click the "submit" button. On the following page, click the "chr21" link in the custom track listing to view the hic track in the Genome Browser.
In this example, you will load a hub that has hic data described in a hub's trackDb.txt file. First, navigate to the Basic Hub Quick Start Guide and review an introduction to hubs.
Visualizing hic files in hubs involves creating three text files: hub.txt, genomes.txt, and trackDb.txt. The browser is passed a URL to the top-level hub.txt file that points to the related genomes.txt and trackDb.txt files. The trackDb.txt file contains stanzas for each track that outlines the details and type of each track to display, such as these lines for a hic file located at the bigDataUrl location:
track hic1
-bigDataUrl http://http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/hic/GSE63525_GM12878_insitu_primary+replicate_combined.hic
+bigDataUrl http://http://hgdownload.gi.ucsc.edu/gbdb/hg19/bbi/hic/GSE63525_GM12878_insitu_primary+replicate_combined.hic
shortLabel hic example
longLabel This hic file shows in situ Hi-C data from Rao et al. (2014) on the GM12878 cell line
type hic
visibility dense
Note: there is now a useOneFile on hub setting that allows the hub
properties to be specified in a single file. More information about this setting can be found on the
Genome Browser User Guide.
Here is a direct link to the trackDb.txt file to see more information about this example hub, and below is a direct link to visualize the hub in the browser, where this example hic file displays in dense mode alongside the other tracks in this hub. You can find more Track Hub hic display options on the Track Database (trackDb) Definition Document page.