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 @@ -1,146 +1,136 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser hic Track Format" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>hic Track Format</h1> <p> <a href="https://github.com/aidenlab/juicer/wiki/Data/#hic-files" target="_blank">Hic format</a> is an indexed binary format designed to permit fast random access to contact matrix heatmaps. The format was designed by the <a href="https://www.aidenlab.org/" target="_blank">Aiden Lab</a> at <a href="https://www.bcm.edu/" target="_blank">Baylor College of Medicine</a>. </p><p> The format is used for displaying chromatin conformation data in the browser. After running a chromatin conformation experiment like in situ Hi-C, researchers can pass their results through the <a href="https://github.com/aidenlab/juicer/wiki" target="_blank">Juicer</a> 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 <a href="hgTrackHubHelp.html#Hosting">Hosting</a> section of the Track Hub Help documentation.</p> <p>The UCSC tools currently support hic versions 6-8.</p> <h2>Generating a hic track</h2> <p> The typical workflow for generating a hic custom track is this:</p> <ol> <li> Prepare your data by processing it with the <a href= "https://github.com/aidenlab/juicer/wiki" target="_blank">Juicer</a> pipeline to create a file in the hic format. </li> <li> Move the hic file (<em>my.hic</em>) to an http, https, or ftp location.</li> <li> Construct a <a href="hgTracksHelp.html#CustomTracks">custom track</a> using a single <a href="hgTracksHelp.html#TRACK">track line</a>. The basic version of the track line will look something like this: <pre><code>track type=hic name="My HIC" bigDataUrl=<em>http://myorg.edu/mylab/my.hic</em></code></pre> </li> <li> Paste the custom track line into the text box in the <a href="../../cgi-bin/hgCustom" target="_blank">custom track management page</a>, click "submit" and view in the Genome Browser.</li> </ol> <h2>Parameters for hic custom track definition lines</h2> <p> All options are placed in a single line separated by spaces (lines are broken only for readability here):</p> <pre><code><strong>track type=hic bigDataUrl=</strong><em>http://...</em> <strong>name=</strong><em>track_label</em> <strong>description=</strong><em>center_label</em> <strong>visibility=</strong><em>display_mode</em> <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>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 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> <pre><code><a href="../../cgi-bin/hgTracks?db=hg19&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt" target="_blank">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt</a> </code></pre> <h2>Sharing Your Data with Others</h2> <p> 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 <a href="https://hgwdev-jcasper.gi.ucsc.edu/goldenPath/help/hgSessionHelp.html#Create">here</a>. 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 <strong>Example 6</strong> on the <a href="customTrack.html#SHARE">custom tracks</a> page.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->