aae00b649b9a851344f98015dd192ac9b2ddc31d dschmelt Wed Nov 13 13:46:22 2019 -0800 Changing Hic citation to minimalist style refs #22316 diff --git src/hg/htdocs/goldenPath/help/hic.html src/hg/htdocs/goldenPath/help/hic.html index f524c9d..dbdffff 100755 --- src/hg/htdocs/goldenPath/help/hic.html +++ src/hg/htdocs/goldenPath/help/hic.html @@ -63,57 +63,47 @@ <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>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. Data cited at the bottom.</p> +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 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.soe.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> -<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 -href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635824/" target="_blank">PMC5635824</a> -</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.soe.ucsc.edu/gbdb/hg19/bbi/hic/GSE63525_GM12878_insitu_primary+replicate_combined.hic shortLabel hic example