f49623d03093fdc8e7f06b65abb0b77efad6a3b9 Merge parents bbabbd5d256 7ec5fd8d353 mspeir Sun Oct 26 12:19:55 2025 -0700 fixed merge conflict. diff --cc src/hg/htdocs/goldenPath/help/hubBasics.html index 9ddd7a5821a,19df6a02d91..e09ea0f79b0 --- src/hg/htdocs/goldenPath/help/hubBasics.html +++ src/hg/htdocs/goldenPath/help/hubBasics.html @@@ -68,69 -68,70 +68,76 @@@ # shortLabels should be under 20 characters and longLabels under 70 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 - corresponding plain-text formats. Together they should cover much + 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 of what you might want to display in the Genome Browser, from transcription peaks to - RNA-seq results. + 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 set of 12 standard fields (though not necessarily all of them), but + 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> - Next, we'll discuss how to build a bigBed from a bed file. <ol> <li>Download the <code>bedToBigBed</code> utility for your system type from - our <a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">download + 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 + 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> @@@ -174,63 -177,64 +183,64 @@@ <p> And here is what that track looks like in the Genome Browser: <br> <img src="/images/bigBedCommonSettings.png"> <p> These common settings added options to the track configuration pop-up: <br> <img src="/images/bigBedCommonSettingsPopUp.png"> <h2>bigWig Tracks</h2> <p> You can use <a href="bigWig.html">bigWig</a> to tracks to display continuous annotations, such as RNA-seq expression, conservation scores, or other - genome-wide scores. You can build a bigWig using one of two plain-text formats: + genome signal scores. You can build a bigWig using one of two plain-text formats: <a href="wiggle.html" target="_blank">wiggle</a> or <a href="bedgraph.html" target="_blank">bedGraph</a>. <h3>Building a bigWig</h3> <p> - Next, we'll discuss how to build a bigWig from a wig or bedGraph file. <ol> <li>Download the <code>wigToBigWig</code> utility for your system type from - our <a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">download + our <a href="https://hgdownload.gi.ucsc.edu/downloads.html#utilities_downloads">download server</a>. <li>Use this utility to build your bigWig: <pre><code>wigToBigWig in.bedGraph chrom.sizes myBigWig.bw</code></pre> <ul> <li>If your assembly is a UCSC-hosted assembly (e.g. hg38), chrom.sizes can - 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 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 + 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 - all tracks required the same basic settings (<code>track, shortLabel, longLabel, type, bigDataUrl</code>). + 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: <ul> <li>"bigWig" is the basic track type <li>"-20 10.003" indicates the minimum and maximum of the data in the bigWig </ul>