cf8b165f6f368e7b0add78408339b203e227715c gperez2 Wed Jul 16 11:37:09 2025 -0700 Updating the bedMethy/bigMethly help page links, refs #36002 diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html index 8872e54f3f4..74e2d210dfc 100755 --- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html +++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html @@ -434,31 +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="bedMethyl.html#bigMethyl">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 @@ -480,31 +480,31 @@ (<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 + See the <a href="bedMethyl.html#bigMethyl">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>