97805fb2ceb73357aa78aa94107148dc355d4e1c mspeir Tue Sep 22 08:36:22 2026 -0700 Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/human/hg38/cons470way.html src/hg/makeDb/trackDb/human/hg38/cons470way.html index 9aa4d7b67f4..bcd97cbac96 100644 --- src/hg/makeDb/trackDb/human/hg38/cons470way.html +++ src/hg/makeDb/trackDb/human/hg38/cons470way.html @@ -3339,43 +3339,30 @@ <th style='text-align:left;'>Ornithorhynchus anatinus</th> <th style='text-align:left;'><a href='https://www.ncbi.nlm.nih.gov/assembly/GCA_004115215.1' target=_blank>HLornAna3 GCA_004115215.1</a></th> <th style='text-align:right;'><a href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9258' target=_blank>9258</a></th> </tr> <tr><th>470</th> <th style='text-align:left;'>Australian echidna</th> <th>Monotremata</th> <th style='text-align:left;'>Tachyglossus aculeatus</th> <th style='text-align:left;'><a href='https://www.ncbi.nlm.nih.gov/assembly/GCA_015852505.1' target=_blank>HLtacAcu1 GCA_015852505.1</a></th> <th style='text-align:right;'><a href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9261' target=_blank>9261</a></th> </tr> </table><br> <b>Table 1.</b> <em>Genome assemblies included in the 470-way Conservation track.</em> </blockquote></p> -<h2>Data Access</h2> -<p> -Downloads for data in this track are available: -<ul> -<li> -<a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz470way/" target=_blank>Multiz alignments</a> (bigMaf and MAF format), and phylogenetic trees</li> -<li> -<a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP470way/" target=_blank>PhyloP conservation</a> (bigWig and WIG format)</li> -<li> -<a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phastCons470way/" target=_blank>PhastCons conservation</a> (bigWig and WIG format)</li> -</ul> - - <h2>Display Conventions and Configuration</h2> <p> In full and pack display modes, conservation scores are displayed as a <em>wiggle track</em> (histogram) in which the height reflects the size of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the <a href="../goldenPath/help/hgWiggleTrackHelp.html" target=_blank>Graph configuration help</a> link for an explanation of the configuration options.</p> <p> Pairwise alignments of each species to the $organism genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using @@ -3516,30 +3503,62 @@ </p> <h3> PhyloP Conservation </h3> <p> The phyloP program supports several different methods for computing p-values of conservation or acceleration, for individual nucleotides or larger elements (<a href="http://compgen.cshl.edu/phast/" target="_blank"> http://compgen.cshl.edu/phast/</a>). Here it was used to produce separate scores at each base (--wig-scores option), considering all branches of the phylogeny rather than a particular subtree or lineage (i.e., the --subtree option was not used). The scores were computed by performing a likelihood ratio test at each alignment column (--method LRT), and scores for both conservation and acceleration were produced (--mode CONACC). </p> +<h2>Data Access</h2> +<p> +The alignments and the conservation scores can be retrieved for a single region or for a list of +regions with the <a +href="hgTables?db=hg38&hgta_group=compGeno&hgta_track=cons470way">Table Browser</a>, +which returns the alignments in MAF format and the scores as wiggle data. The scores and the +conserved elements, though not the alignments, can also be joined with other annotations in the +<a href="hgIntegrator?db=hg38">Data Integrator</a>. For automated access, our <a +href="../goldenPath/help/api.html">REST API</a> serves the alignment and conservation tracks +individually, by name. +</p> +<p> +Downloads for data in this track are available: +<ul> +<li> +<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz470way/" target=_blank>Multiz alignments</a> (bigMaf and MAF format), and phylogenetic trees</li> +<li> +<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP470way/" target=_blank>PhyloP conservation</a> (bigWig and WIG format)</li> +<li> +<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phastCons470way/" target=_blank>PhastCons conservation</a> (bigWig and WIG format)</li> +</ul> +</p> +<p> +Genome-wide alignment and conservation files are large. Among our command-line programs, +<tt>mafsInRegion</tt>, <tt>mafSpeciesSubset</tt> and <tt>mafFrags</tt> pull out a region, a +subset of species, or the alignment underlying a gene, and <tt>bigWigToWig</tt> and +<tt>bigWigSummary</tt> read the conservation files. They can be downloaded from the <a +href="https://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank">utilities directory</a>, and +each one prints its usage when run with no arguments. See our <a +href="../FAQ/FAQdownloads.html">Data Access FAQ</a> for more information. +</p> + <h2>Credits</h2> <p> This track was created using the following programs: <ul> <li> Alignment tools: lastz (formerly blastz) and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the <a href="http://www.bx.psu.edu/miller_lab/" target=_blank>Penn State Bioinformatics Group</a> <li> Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC <li> Conservation scoring: phastCons, phyloP, phyloFit, tree_doctor, msa_view and other programs in PHAST by <a href="https://siepellab.labsites.cshl.edu/" target=_blank>Adam Siepel</a> at Cold Spring Harbor Laboratory (original development done at the Haussler lab at UCSC). <li> MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC <li> Tree image generator: phyloPng by Galt Barber, UCSC