9a051963c7dc7cafea316417701cae4570aff029 braney Sun Jul 13 13:07:07 2025 -0700 templates for bedMethyl and bigMethyl diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html index 09da8021cb0..8872e54f3f4 100755 --- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html +++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html @@ -78,31 +78,31 @@ are a useful tool for visualizing a large number of genome-wide data sets. For example, a project that has produced several wiggle plots of data can use the hub utility to organize the tracks into composite and super-tracks, making it possible to show the data for a large collection of tissues and experimental conditions in a visually elegant way, similar to how the ENCODE native data tracks are displayed in the browser.</p> <p> The track hub utility allows efficient access to data sets from around the world through the familiar Genome Browser interface. Browser users can display tracks from any public track hub that has been registered with UCSC. Additionally, users can import data from unlisted hubs or can set up, display, and share their own track hubs. Genome assemblies that UCSC does not support can be loaded and viewed with associated data.</p> <p> The data underlying the tracks and optional sequence in a hub reside on the remote server of the data provider rather than at UCSC. Genomic annotations are stored in compressed binary indexed files in bigBed, bigBarChart, bigGenePred, -bigNarrowPeak, bigPsl, bigChain, bigInteract, bigMaf, bigWig, BAM, CRAM, HAL, +bigNarrowPeak, bigMethyl, bigPsl, bigChain, bigInteract, bigMaf, bigWig, BAM, CRAM, HAL, hic or VCF format that contain the data at several resolutions. In the case of assemblies that UCSC does not support, genomic sequence is stored in the efficient twoBit format. When a hub track is displayed in the Genome Browser, only the relevant data needed to support the view of the current genomic region are transmitted rather than the entire file. The transmitted data are cached on the UCSC server to expedite future access. This on-demand transfer mechanism eliminates the need to transmit large data sets across the Internet, thereby minimizing upload time into the browser.</p> <p> The track hub utility offers a convenient way to view and share very large sets of data. Individuals wishing to display only a few small data sets may find it easier to use the Genome Browser <a href="hgTracksHelp.html#CustomTracks">custom track</a> utility. As with hub tracks, custom tracks can be uploaded to the UCSC Genome Browser and viewed alongside the native annotation tracks. Custom tracks can be constructed from a wide range of data types; hub tracks are limited to compressed binary indexed formats that can be remotely hosted. However, the custom tracks utility does not @@ -364,31 +364,31 @@ <a href="/cgi-bin/hgTracks?genome=GCA_002844635.1&hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubGenArkExample/genArkTrackHub/hub.txt" target="_blank">https://genome.ucsc.edu/cgi-bin/hgTracks?genome=GCA_002844635.1&hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubGenArkExample/genArkTrackHub/hub.txt</a> </pre> <!-- ========== Setting Up Your Own Track Hub ============================== --> <a name="Setup"></a> <h2>Setting up your own Track Hub</h2> <p> This section provides a step-by-step description of the process used to set up a track hub on your own server. If you would like information about how to attach a track hub to an existing assembly hub, please refer to the following <a href="/FAQ/FAQlink.html#trackHubLoading">FAQ entry</a>.</p> <p> To create your own hub you will need:</p> <ul> <li> one or more data sets formatted in one of the compressed binary index formats supported by the - Genome Browser: bigBed, bigBarChart, bigGenePred, bigNarrowPeak, bigPsl, bigChain, bigInteract, + Genome Browser: bigBed, bigBarChart, bigGenePred, bigNarrowPeak, bigMethyl, bigPsl, bigChain, bigInteract, bigMaf, bigWig, BAM, CRAM, HAL, hic or VCF</li> <li> a set of text files that specify properties for the track hub and for each of the data tracks within it</li> <li> a twoBit file with your sequence if you are setting up an assembly hub. Note that the allowed characters in sequence names are [A-Za-z_0-9_-]</li> <li> an Internet-enabled web server or ftp server </li> <!--Question: do we have some general minimum requirements for this?--> </ul> <p> The files are placed on the server in a file hierarchy like the one shown in <em>Example 1</em>. Users experienced in setting up Genome Browser mirrors that contain their own data will find that setting up a track hub is similar, but is usually much easier. Depending on the number and @@ -434,30 +434,31 @@ rnaSeq.html - description text for an RNAseq track rnaSeqLiver.bigWig - wiggle plot of RNAseq data in liver rnaSeqLiver.bigBed - intron/exon lists for liver rnaSeqLung.bigWig - wiggle plot of RNAseq data in lung rnaSeqLung.bigBed - intron/exon lists for lung </code></pre> <hr> <p> <strong>Step 1. Format the data</strong><br> The data tracks provided by a hub must be formatted in one of the compressed binary index formats supported by the Genome Browser: <a href="bigWig.html">bigWig</a>, <a href="bigBed.html">bigBed</a>, <a href="bigGenePred.html">bigGenePred</a>, <a href="bigChain.html">bigChain</a>, <a href="bigNarrowPeak.html">bigNarrowPeak</a>, +<a href="bigMethyl.html">bigMethyl</a>, <a href="barChart.html">bigBarChart</a>, <a href="interact.html">bigInteract</a>, <a href="bigPsl.html">bigPsl</a>, <a href="bigMaf.html">bigMaf</a>, <a href="hic.html">hic</a>, <a href="bam.html">BAM</a>, <a href="cram.html">CRAM</a>, <a href="https://github.com/ComparativeGenomicsToolkit/hal" target="_blank">HAL</a> or <a href="vcf.html">VCF</a>. Many of these formats also support several different <a href="/FAQ/FAQcustom.html#custom12">chromosome aliases</a> (e.g. '1' or 'NC_000001.11' in place of 'chr1'). </p> <p> <em>bigWig</em> - The bigWig format is best for displaying continuous value plot data, such as @@ -476,30 +477,36 @@ information on creating and configuring bigBed tracks.</p> <p> <em>bigGenePred</em> - BigGenePred files are binary indexed versions of Browser Extensible Data (<a href="../../FAQ/FAQformat.html#format1">BED</a>) files with an extra eight fields that are useful for describing gene predictions that are modeled after the fields in <a href="../../FAQ/FAQformat.html#format9">genePred</a> files. BigGenePred format is useful for associating a name and (optionally) a color and a score with one or more related regions on the same chromosome, such as all the exons of a gene. See the <a href="bigGenePred.html">bigGenePred Track Format</a> help page for information on creating and configuring bigGenePred tracks.</p> <p> <em>bigChain</em> - BigChain files are binary indexed versions of <a href="chain.html">chain</a> files. BigChain format is useful for large pairwise alignment data sets. See the <a href="bigChain.html">bigChain Track Format</a> help page for more information on creating and configuring bigChain tracks.</p> <p> +<em>bigMethyl</em> - BigMethyl files are binary indexed versions of Browser Extensible Data +(<a href="../../FAQ/FAQformat.html#format1">BED</a>) files with first nine fields being the same as bed, +and an extra nine fields that contain various scores. + See the <a href="bigMethyl.html">bigMethyl Track +Format</a> help page for information on creating and configuring bigMethyl tracks.</p> +<p> <em>bigNarrowPeak</em> - BigNarrowPeak files are binary indexed versions of Browser Extensible Data (<a href="../../FAQ/FAQformat.html#format1">BED</a>) files with first six fields being the same as bed, and an extra four fields that contain various scores and the offset of the base within the block that is the peak. See the <a href="bigNarrowPeak.html">bigNarrowPeak Track Format</a> help page for information on creating and configuring bigNarrowPeak tracks.</p> <p> <em>bigBarChart</em> - BigBarChart files are binary indexed versions of <a href="../../FAQ/FAQformat.html#format21">barChart</a> files. BigBarChart format is useful for bringing barChart display into track hubs, and supports schema customization and label configuration that is not supported for regular barChart format. See the <a href="barChart.html">barChart Track Format</a> help page for information on creating and configuring bigBarChart tracks.</p> <p> <em>bigInteract</em> - BigInteract files are binary indexed versions of <a href="../../FAQ/FAQformat.html#format22">interact</a> files. BigInteract format is useful for