198c9b8daecc44fbda6a6494c566c723920f030a lrnassar Wed Mar 11 18:25:21 2026 -0700 Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM. diff --git src/hg/htdocs/goldenPath/help/hic.html src/hg/htdocs/goldenPath/help/hic.html index 1e00c466408..58e45036e37 100755 --- src/hg/htdocs/goldenPath/help/hic.html +++ src/hg/htdocs/goldenPath/help/hic.html @@ -78,57 +78,57 @@ <strong>description </strong><em>center label </em> # default is "User Supplied Track" <strong>visibility </strong><em>full|dense|hide </em> # default is hide (will also take numeric values 4|1|0) <strong>db </strong><em>genome database </em> # e.g. hg19 for Human Feb. 2009 (GRCh37) </code></pre> <p>Note that hic tracks currently only support the full, dense, and hide visibility modes. The <a target="_blank" href="hgHicTrackHelp.html">hic track configuration</a> help page describes the hic track configuration page options.</p> <h3>Example #1</h3> <p> 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).</p> <p> The line breaks inserted in the track line for readability must be removed before submitting this entry as a Custom Track. Click <a href="examples/hicExampleOne.txt">here</a> for a -text version you can paste without editing. The "browser" line above is used set +text version you can paste without editing. The "browser" line above is used to set the default view to a region of chromosome 21.</p> <pre><code>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</code></pre> <p> Paste the "browser" line and "track" line into the <a href="../../cgi-bin/hgCustom" target="_blank">custom track management page</a> 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.</p> <h3>Example #2</h3> <p> In this example, you will load a hub that has hic data described in a hub's trackDb.txt file. First, navigate to the <a href="hubQuickStart.html" target="_blank">Basic Hub Quick Start Guide</a> and review an introduction to hubs.</p> <p> Visualizing hic files in hubs involves creating three text files: <em>hub.txt</em>, <em>genomes.txt</em>, and <em>trackDb.txt</em>. The browser is passed a URL to the top-level <em>hub.txt</em> file that points to the related <em>genomes.txt</em> and <em>trackDb.txt</em> files. The <em>trackDb.txt</em> 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:</p> <pre><code>track hic1 -bigDataUrl http://http://hgdownload.gi.ucsc.edu/gbdb/hg19/bbi/hic/GSE63525_GM12878_insitu_primary+replicate_combined.hic +bigDataUrl 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</code></pre> <p> <b>Note:</b> there is now a <code>useOneFile on</code> hub setting that allows the hub properties to be specified in a single file. More information about this setting can be found on the <a href="./hgTracksHelp.html#UseOneFile" target="_blank">Genome Browser User Guide</a>.</p> <p> Here is a direct link to the <em><a href="examples/hubDirectory/hg19/trackDb.txt" target="_blank">trackDb.txt</a></em> 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 <a href="trackDb/trackDbHub.html#hic" target="_blank">Track Database (trackDb) Definition Document</a> page.</p>