817ed6c4b137f61c521d8d1289dd38823df78ba7 gperez2 Fri Nov 7 16:06:40 2025 -0800 Fixing some typos and making some edits, refs #28347 diff --git src/hg/htdocs/goldenPath/help/hubBasics.html src/hg/htdocs/goldenPath/help/hubBasics.html index e09ea0f79b0..772e5035124 100755 --- src/hg/htdocs/goldenPath/help/hubBasics.html +++ src/hg/htdocs/goldenPath/help/hubBasics.html @@ -69,107 +69,100 @@ shortLabel Example Hub longLabel Example Hub for useOneFile option useOneFile on email genome-www@soe.ucsc.edu genome hg38 </pre></code> <p> If you have tracks across multiple assemblies, see the <a href="hgTrackHubHelp.html">full track hub documentation</a>.</p> <a name="types"></a> <h2>Common Track Types</h2> <p> The most common <a href="/FAQ/FAQformat.html">track types</a> are bigBed and bigWig. Compressed, binary versions of -the corresponding plain-text formats. Together they should cover most +the corresponding plain-text formats. Together, they should cover most of what you might want to display in the Genome Browser, from transcription peaks to RNA-seq signals. <h2>bigBed Tracks</h2> <p> You can use <a href="bigBed.html">bigBed</a> tracks to display discrete annotations, such as genes, transcription start sites, or conserved genomic elements. The bigBed format builds off the plain-text <a href="/FAQ/FAQformat.html#format1">BED format</a> and is thus flexible in terms of what fields are included. Your file must start with a minimum of 3, and up to 12, standard fields, but can also extend the format with any number of additional fields. <h3>Building a bigBed</h3> <p> <ol> <li>Download the <code>bedToBigBed</code> utility for your system type from our <a href="https://hgdownload.gi.ucsc.edu/downloads.html#utilities_downloads">download server</a>. <li>Use <code>bedToBigBed</code> to build your bigBed: <pre><code>bedToBigBed -sort in.bed chrom.sizes myBigBed.bb</code></pre> <ul> <li>If your assembly is a UCSC-hosted assembly (e.g. hg38), chrom.sizes can -<<<<<<< HEAD be a URL (replace "genNom" with the assembly name (e.g. hg38)): http://hgdownload.gi.ucsc.edu/goldenPath/genNom/bigZips/genNom.chrom.sizes. - If you're working with a GenArk assembly hub, then the chrom.sizes -======= - be a URL (e.g. hg38): - <a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes"> - https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes</a>. If you're working with a <a href="https://hgdownload.soe.ucsc.edu/hubs/"> GenArk assembly hub</a> (e.g. GCF/GCA), then the chrom.sizes ->>>>>>> 7ec5fd8d353ae3486915167a5d57c84cb0cb918f file can be found under the "Data file downloads" section on the <a href="/cgi-bin/hgGateway" target="_blank">assembly gateway page</a>. <li>If you have custom fields in your bed file, you will need to create a custom .as file. You can download the <a href="examples/bed12.as">basic BED .as</a> and modify this by adding new fields below those in your file. </ul> <li>Put your bigBed file alongside your hub.txt in a web-accessible location, either through <a href="/cgi-bin/hgHubConnect#hubUpload">the 10GB of space we make available to users</a> or through one of <a href="hgTrackHubHelp#Hosting">several other services</a>. <li>You will use the file name (e.g. "myBigBed.bb") with the <code>bigDataUrl</code> setting in your hub.txt. </ol> <h3>bigBed track hub configuration</h3> <p> Once you have built your bigBed files, it is time to create a stanza in your hub.txt file for that track. Here is what the required settings discussed above might look like for a basic bigBed track: <p> <pre><code>track bigBedRequiredSettings shortLabel bigBed Required Settings longLabel A bigBed Example with Required Settings visibility pack type bigBed 12 + bigDataUrl gtexCaviar.chr7_155799529-155812871.bb </code></pre> -<p>The type line consists of three parts: +<p>The <code>type</code> line consists of three parts: <ul> <li>"bigBed" is the basic track type. <li>"12" indicates how many standard BED fields are included in your file. You may need to change this to match the number of standard BED fields in your file. <li>"+" tells the genome browser there are extra fields beyond the standard fields. If your file has no extra fields, replace this with a "." (e.g. type bigBed 12 .). </ul> <p>Here is a screenshot of what this basic bigBed track looks like displayed in the Genome Browser: <br> <img src="/images/bigBedReqSettings.png"> <p> -The bigBed format also offer a wide range of customization options for the -display, from decorators to highlights. Additionally, it offer extensive +The bigBed format also offers a wide range of customization options for the +display, from decorators to highlights. Additionally, it offers extensive <a href="/goldenPath/help/hubQuickStartFilter.html"> filter controls</a>, <a href="/goldenPath/help/hubQuickStartSearch.html"> searching options</a>, and mouseover configurations. Our <a href="trackDb/trackDbHub.html" target="_blank">trackDb documentation</a> contains a full listing of settings available for the format. <p> Here is the bigBed configuration with some commonly used settings, including filtering and mouseover configuration. <p><pre><code>track bigBedCommonSettings shortLabel bigBed Common Settings longLabel A bigBed Example with Commonly Used Settings visibility pack type bigBed 12 + @@ -215,64 +208,64 @@ https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes</a>. If you're working with a <a href="https://hgdownload.soe.ucsc.edu/hubs/"> GenArk assembly hub</a> (e.g. GCF/GCA), then the chrom.sizes file can be found under the "Data file downloads" section on the <a href="/cgi-bin/hgGateway" target="_blank">assembly gateway page</a>. </ul> <li>Put your bigWig file alongside your hub.txt in a web-accessible location, either through <a href="/cgi-bin/hgHubConnect#hubUpload">the 10GB of space we make available to users</a> or through one of <a href="hgTrackHubHelp#Hosting">several other services</a>. <li>You will use the file name (e.g. "myBigWig.bw") with the <code>bigDataUrl</code> setting. </ol> <h3>bigWig track hub configuration</h3> <p> -The basic trackDb configuration for a bigWig track is similar to a bigBed track as +The basic trackDb configuration for a bigWig track is similar to a bigBed track, as all tracks require the same basic settings (<code>track, shortLabel, longLabel, type, bigDataUrl</code>). This is what the configuration for a bigWig track might look like (the example hub.txt includes other useful settings): <p><pre><code>track bigWigExample shortLabel bigWig Example longLabel A bigWig Example with Commonly Used Settings visibility pack type bigWig -20 10.003 bigDataUrl hg38.phyloP100way.chr7_155799529-155812871.bw color 60,60,140 </code></pre> -<p>The type line consists of two parts: +<p>The <code>type</code> line consists of two parts: <ul> <li>"bigWig" is the basic track type <li>"-20 10.003" indicates the minimum and maximum of the data in the bigWig </ul> <p> Here is what this looks like visualized in the Genome Browser: <br> <img src="/images/bigWigReqSettings.png"> <a name="grouping"></a> <h2>Grouping tracks</h2> <p> Next, we'll provide a basic overview of how to group your tracks using composite tracks and super tracks. This will allow you to pull similar data together under a single container. <h3>Composite Tracks</h3> <p> Composite tracks can hold multiple tracks of the same type. For example, you -use a composite to group together a set of RNA-seq experiments including +use a composite to group together a set of RNA-seq experiments, including replicates. <p> Here's what the configuration might look like for a composite containing two bigWig tracks. There are two key components of a composite: (1) the line "compositeTrack on" in the parent track stanza, and (2) including "parent compositeName" for each track that will be part of the composite. <p><pre><code>track compositeExample shortLabel Example Composite Track longLabel Example composite track using bigWigs visibility dense type bigWig compositeTrack on track compositeBigWig1 @@ -338,45 +331,47 @@ bigDataUrl a.chr7_155799529-155812871.bw shortLabel ST bigWig composite #1 longLabel A composite-contained bigWig in a super track example #1 parent superTrackCompositeBigWig on type bigWig 0 1 track superTrackCompositeBigWig2 bigDataUrl c.chr7_155799529-155812871.bw shortLabel ST bigWig composite #2 longLabel A composite-contained bigWig in a super track example #2 parent superTrackCompositeBigWig on type bigWig 0 1 </code></pre> <p> -Loading the example hub with this super track onfiguration looks like this: +Loading the example hub with this super track configuration looks like this: <br> <img src="/images/superTrackEx.png"> <a name="description"></a> <h2>Creating description pages</h2> <p> If you plan to share your track hub more widely, you will want to create a description page for your tracks. A description page could contain a short description of what the data represents, how the data was generated, -a link to the associated paper, or a contact email for questions regarding the data. +a link to the associated paper, or a contact email for questions regarding the data. Multiple tracks can use +the same description page. + <p> We provide an <a href="examples/hubExamples/templatePage.html">example description html</a> that you can modify with the details for your track. Once you've modified this example html for your -track add an <code>html</code> to the corresponding track stanza: +track, add an <code>html</code> to the corresponding track stanza: <p><pre><code>track bigWigExample shortLabel bigWig Example longLabel A bigWig Example with Commonly Used Settings type bigWig -20 10.003 bigDataUrl hg38.phyloP100way.chr7_155799529-155812871.bw html bigWigDescription.html </code></pre> <a name="sharing"></a> <h2>Sharing your hub</h2> <p> Once you have a functional hub that you would like to share with others, you can create links that you give to others in two ways. <p> @@ -385,28 +380,28 @@ Load your hub, configure the genome browser as you'd like (e.g. position and data tracks), select "My Sessions" under "My Data", and use the option to save the current settings as a session. You will then be provided with a URL that you can share with others. <p> The other option is to create a URL to the Genome Browser that loads your hub on the assembly of interest. There are three <a href="/FAQ/FAQlink.html">URL parameters</a> you will want to use: <ul> <li><code>db</code> - UCSC assembly name (e.g. hg38) <li><code>position</code> - chromosome position to load <li><code>hubUrl</code> - URL to your hub </ul> <p> -You will then append these to a genome browser URL. For example, this url with load the example hub: +You will then append these to a genome browser URL. For example, this url loads the example hub: <pre><code>https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr7:155799529-155812871&hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubBasicSettings/hub.txt </code></pre> <p> If you feel that your hub would be of general use to the research community, you can contact us about making it a public hub. Note that public hubs have to meet more stringent requirements than the basics described here. Check that your hub meets the <a href="publicHubGuidelines.html">public hub requirements</a> and then follow the directions on that page for submitting it to us for review. <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->