e5759993329b6e609e9ab825991a90283e714088 mspeir Wed Sep 9 11:17:57 2026 -0700 Help pages: fix broken internal links and restore anchors people still cite, refs #38062 Three groups of anchor problems on the help and FAQ pages. Broken internal links, five pages: posters.html listed a 2022 section that does not exist (no 2022 posters), api.html listed REST and JSON separately after the two sections were merged, docker.html pointed at a #UsrAcct section that is not on that page, FAQgenes.html had a capitalized #ncbiRefSeq where the anchor is #ncbiRefseq, and the genomes.txt settings rows in trackDbHub.v3.html carried no anchors so its own "genome" link missed. Retired anchors that are still cited in twenty years of answers on the genome list. Content moved to its own page and the old anchor was deleted rather than left behind, so the citations land at the top of the page. Reattached seven numeric FAQformat anchors to the Topics entry linking to each format's page. BED, PSL, GFF and GTF were removed from the custom track page in 2012 and never added back to its list of supported formats; added them with the old anchors, which fixes customTrack.html and hgTracksHelp.html together since both include customTrackText.html. Also restored #lines there, and #Session on hgTrackHubHelp.html and #link4 on FAQlink.html. Section anchors on six pages that had none, so a support answer can link to one part of them: bam.html, hic.html, bedgraph.html, ftp.html, net.html and trackDbIndexBb.html. Skipped quickLiftChain.html, oligoMatch.html and cutters.html, which are track description fragments included into the details page rather than standalone pages. Co-Authored-By: Claude Opus 5 (1M context) diff --git src/hg/htdocs/goldenPath/help/hic.html src/hg/htdocs/goldenPath/help/hic.html index fc592dc1b4f..923257f1db1 100755 --- src/hg/htdocs/goldenPath/help/hic.html +++ src/hg/htdocs/goldenPath/help/hic.html @@ -22,99 +22,103 @@ The format is used for displaying chromatin conformation data in the browser. This format is useful for displaying interactions at a scale and depth that exceeds what can be easily visualized with the interact and bigInteract formats. After running a chromatin conformation experiment such as in situ Hi-C, researchers can pass their results through the Juicer pipeline to produce a hic file. Due to the large size of many of these files, UCSC is not able to support direct upload via our Custom Track interface. Instead, users should place their Hic files in a web-accessible space and enter the URL as a bigDataUrl. If you do not have access to a web-accessible server and need hosting space for your Hic files, please see the Hosting section of the Track Hub Help documentation.

Generating a hic track

The typical workflow for generating a hic custom track is this:

Prepare your data by processing it with the Juicer pipeline to create a file in the hic format.
Move the hic file (my.hic) to an http, https, or ftp location.
Construct a custom track using a single track line. The basic version of the track line will look something like this:
```
track type=hic name="My HIC" bigDataUrl=http://myorg.edu/mylab/my.hic
```
Paste the custom track line into the text box in the custom track management page, click "submit" and view in the Genome Browser.

Parameters for hic custom track definition lines

All options are placed in a single line separated by spaces (lines are broken only for readability here):

track type=hic bigDataUrl=http://...
     name=track_label
     description=center_label 
     visibility=display_mode
     db=db

Note if you copy/paste the above example, you must remove the line breaks. Click here for a text version that you can paste without editing.

The track type and bigDataUrl are REQUIRED:

type=hic bigDataUrl=http://myorg.edu/mylab/my.hic

The remaining settings are OPTIONAL:

name            track label                 # default is "User Track"
 description     center label                # default is "User Supplied Track"
 visibility      full|dense|hide             # default is hide (will also take numeric values 4|1|0)
 db              genome database             # e.g. hg19 for Human Feb. 2009 (GRCh37)

Note that hic tracks currently only support the full, dense, and hide visibility modes. The hic track configuration help page describes the hic track configuration page options.

Example #1

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 to 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.gi.ucsc.edu/gbdb/hg19/bbi/hic/GSE63525_HMEC_combined.hic

Paste 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.

Example #2

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 https://hgdownload.gi.ucsc.edu/gbdb/hg19/bbi/hic/GSE63525_GM12878_insitu_primary+replicate_combined.hic
 shortLabel hic example
@@ -128,25 +132,26 @@
 
 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.
 http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt 
 
   
    
   
 
 
+
 Sharing Your Data with Others
 
 If you would like to share your hic data track with a colleague, there are a couple of options.
 One method is to load your data track into the UCSC Genome Browser and then create a saved session
 by following the instructions here.
 If you are looking for a more automated method of sharing data, you may be interested to learn how to create
 a direct URL that loads custom data files.  For a demonstration of this, see Example 6 on the
 custom tracks page.