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/cons7way.html src/hg/makeDb/trackDb/human/hg38/cons7way.html index b79da8f66a4..f8026007e45 100644 --- src/hg/makeDb/trackDb/human/hg38/cons7way.html +++ src/hg/makeDb/trackDb/human/hg38/cons7way.html @@ -49,40 +49,30 @@ level (see <EM>Gap Annotation</EM>, below). </P> <P> <BLOCKQUOTE><TABLE BORDER=1 CELLPADDING=4 BORDERCOLOR="#aaaaaa"> <TR ALIGN=left><TH>Organism</TH><TH>Species</TH><TH>Release date</TH><TH>UCSC version</TH><TH>alignment type</TH></TR> <TR ALIGN=left><TD>Human</TD><TD>Homo sapiens</TD><TD>Dec. 2013</TD><TD><A HREF="../cgi-bin/hgGateway?db=hg38" TARGET=_blank>GRCh38/hg38</A></TD><TD>reference species</TD></TR> <TR ALIGN=left><TD>Chimp</TD><TD>Pan troglodytes</TD><TD>Feb. 2011</TD><TD><A HREF="../cgi-bin/hgGateway?db=panTro4" TARGET=_blank>GSAC 2.1.4/panTro4</A></TD><TD>Syntenic net</TD></TR> <TR ALIGN=left><TD>Rhesus</TD><TD>Macaca mulatta</TD><TD>Oct. 2010</TD><TD><A HREF="../cgi-bin/hgGateway?db=rheMac3" TARGET=_blank>BGI CR 1.0/rheMac3</A></TD><TD>Syntenic net</TD></TR> <TR ALIGN=left><TD>Dog</TD><TD>Canis lupus familiaris</TD><TD>Sep. 2011</TD><TD><A HREF="../cgi-bin/hgGateway?db=canFam3" TARGET=_blank>Broad/canFam3</A></TD><TD>Syntenic net</TD></TR> <TR ALIGN=left><TD>Mouse</TD><TD>Mus musculus</TD><TD>Dec. 2011</TD><TD><A HREF="../cgi-bin/hgGateway?db=mm10" TARGET=_blank>GRCm38/mm10</A></TD><TD>Syntenic net</TD></TR> <TR ALIGN=left><TD>Rat</TD><TD>Rattus norvegicus</TD><TD>Mar. 2012</TD><TD><A HREF="../cgi-bin/hgGateway?db=rn5" TARGET=_blank>RGSC 5.0/rn5</A>*</TD><TD>Syntenic net</TD></TR> <TR ALIGN=left><TD>Opossum</TD><TD>Monodelphis domestica</TD><TD>Oct. 2006</TD><TD><A HREF="../cgi-bin/hgGateway?db=monDom5" TARGET=_blank>Broad/monDom5</A></TD><TD>Net</TD></TR> </TABLE><BR> <B>Table 1.</B> <EM>Genome assemblies included in the 7-way Conservation track.</EM> </BLOCKQUOTE></P> -Downloads for data in this track are available: -<UL> -<LI> -<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz7way/">Multiz alignments</A> (MAF format), and phylogenetic trees -<LI> -<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP7way/">PhyloP conservation</A> (WIG format) -<LI> -<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phastCons7way/">PhastCons conservation</A> (WIG format) -</UL> - <p> (UPDATE May 2015) Note that due to an error while creating the alignments for this track, some of the alignments are missing from some of the unplaced and unlocalized contigs in rhesus, mouse and dog. This problem has been fixed in the subsequent <a href=" ../../cgi-bin/hgTrackUi?db=hg38&g=cons20way">Primate Conservation</a> track and any future Conservation tracks. </p> <H2>Display Conventions and Configuration</H2> <P> The track configuration options allow the user to display the three different sets of scores, all, birds or vertebrate, individually or all simultaneously. In full and pack display modes, conservation scores are displayed as a <EM>wiggle track</EM> (histogram) in which the height reflects the value of the score. @@ -300,30 +290,62 @@ <h3> Conserved Elements </h3> <P> The conserved elements were predicted by running phastCons with the --viterbi option. The predicted elements are segments of the alignment that are likely to have been "generated" by the conserved state of the phylo-HMM. Each element is assigned a log-odds score equal to its log probability under the conserved model minus its log probability under the non-conserved model. The "score" field associated with this track contains transformed log-odds scores, taking values between 0 and 1000. (The scores are transformed using a monotonic function of the form a * log(x) + b.) The raw log odds scores are retained in the "name" field and can be seen on the details page or in the browser when the track's display mode is set to "pack" or "full". </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=cons7way">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/multiz7way/" target="_blank">Multiz alignments</A> (MAF format), and phylogenetic trees +<LI> +<A HREF="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP7way/" target="_blank">PhyloP conservation</A> (WIG format) +<LI> +<A HREF="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phastCons7way/" target="_blank">PhastCons conservation</A> (WIG format) +</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: 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