bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/hubBasics.html src/hg/htdocs/goldenPath/help/hubBasics.html index 143f6668adf..9ddd7a5821a 100755 --- src/hg/htdocs/goldenPath/help/hubBasics.html +++ src/hg/htdocs/goldenPath/help/hubBasics.html @@ -87,38 +87,38 @@ <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 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 be a URL (replace "genNom" with the assembly name (e.g. hg38)): - http://hgdownload.soe.ucsc.edu/goldenPath/genNom/bigZips/genNom.chrom.sizes. + http://hgdownload.gi.ucsc.edu/goldenPath/genNom/bigZips/genNom.chrom.sizes. If you're working with a GenArk assembly hub, 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>. <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> @@ -184,38 +184,38 @@ <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: <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.soe.ucsc.edu/goldenPath/genNom/bigZips/genNom.chrom.sizes. + http://hgdownload.gi.ucsc.edu/goldenPath/genNom/bigZips/genNom.chrom.sizes. If you're working with a GenArk assembly hub, 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 all tracks required the same basic settings (<code>track, shortLabel, longLabel, type, bigDataUrl</code>).