0ac4f70c8e22a3831b01aa51ccc1a5f36bad0b04 jcasper Fri Nov 8 16:58:18 2019 -0800 Minor formatting/corrections, no ticket diff --git src/hg/htdocs/goldenPath/help/hic.html src/hg/htdocs/goldenPath/help/hic.html index d9af502..4712c76 100755 --- src/hg/htdocs/goldenPath/help/hic.html +++ src/hg/htdocs/goldenPath/help/hic.html @@ -58,31 +58,31 @@ <strong>db=</strong><em>db</em></code></pre> <p> Note if you copy/paste the above example, you must remove the line breaks. Click <a href="examples/hicExample.txt">here</a> for a text version that you can paste without editing.</p> <p> The track type and bigDataUrl are REQUIRED:</p> <pre><code><strong>type=hic bigDataUrl=</strong><em>http://myorg.edu/mylab/my.hic</em></strong> </code></pre> <p> The remaining settings are OPTIONAL:</p> <pre><code><strong>name </strong><em>track label </em> # default is "User Track" <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>priority </strong><em>N </em> # default is 100 <strong>db </strong><em>genome database </em> # e.g. hg19 for Human Feb. 2009 (GRCh37) </code></pre> -Note that hic tracks currently only support the full, dense, and hide visibility modes. +<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 server — data from an in situ Hi-C experiment on the HMEC cell line from the following paper, mapped to the hg19 assembly:</p> <p> Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES <em>et al</em>. <a href="https://linkinghub.elsevier.com/retrieve/pii/S0092-8674(14)01497-4" target="_blank"> A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping</a>. <em>Cell</em>. 2014 Dec 18;159(7):1665-80. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/25497547" target="_blank">25497547</a>; PMC: <a