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/birds/geoFor1/cons7way.html src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html index f4d47ea4dba..3497cb8af90 100644 --- src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html +++ src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html @@ -60,40 +60,30 @@ <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>Medium ground finch</TD><TD>Geospiza fortis</TD><TD>Apr. 2012</TD><TD><A HREF="../cgi-bin/hgGateway?db=geoFor1" TARGET=_blank>BGI/geoFor1</A></TD><TD>reference species</TD></TR> <TR><TH COLSPAN=5>Birds subset</TH></TR> <TR ALIGN=left><TD>Budgerigar</TD><TD>Melopsittacus undulatus</TD><TD>Sep. 2011</TD><TD><A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/melUnd1" TARGET=_blank>WUGSC v6.3/melUnd1</A>*</TD><TD>Syntenic net</TD></TR> <TR ALIGN=left><TD>Zebra finch</TD><TD>Taeniopygia guttata</TD><TD>Jul. 2008</TD><TD><A HREF="../cgi-bin/hgGateway?db=taeGut1" TARGET=_blank>WUGSC 3.2.4/taeGut1</A></TD><TD>Net</TD></TR> <TR ALIGN=left><TD>Chicken</TD><TD>Gallus gallus</TD><TD>Nov. 2011</TD><TD><A HREF="../cgi-bin/hgGateway?db=galGal4" TARGET=_blank>ICGSC Gallus_gallus-4.0/galGal4</A></TD><TD>Syntenic net</TD></TR> <TR ALIGN=left><TD>Turkey</TD><TD>Meleagris gallopavo</TD><TD>Dec. 2009</TD><TD><A HREF="../cgi-bin/hgGateway?db=melGal1" TARGET=_blank>TGC Turkey_2.01/melGal1</A></TD><TD>Syntenic net</TD></TR> <TR><TH COLSPAN=5>Vertebrates subset</TH></TR> <TR ALIGN=left><TD>Human</TD><TD>Homo sapiens</TD><TD>Feb. 2009</TD><TD><A HREF="../cgi-bin/hgGateway?db=hg19" TARGET=_blank>GRCh37/hg19</A></TD><TD>Reciprocal best</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>Reciprocal best</TD></TR> </TABLE><BR> <B>Table 1.</B> <EM>Genome assemblies included in the 7-way Conservation track.</EM><BR> * Data download only, browser not available. </BLOCKQUOTE></P> -Downloads for data in this track are available: -<UL> -<LI> -<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/geoFor1/multiz7way/">Multiz alignments</A> (MAF format), and phylogenetic trees -<LI> -<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/geoFor1/phyloP7way/">PhyloP conservation</A> (WIG format) -<LI> -<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/geoFor1/phastCons7way/">PhastCons conservation</A> (WIG format) -</UL> - <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. 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 @@ -313,30 +303,62 @@ <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=geoFor1&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=geoFor1">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/geoFor1/multiz7way/" target="_blank">Multiz alignments</A> (MAF format), and phylogenetic trees +<LI> +<A HREF="https://hgdownload.soe.ucsc.edu/goldenPath/geoFor1/phyloP7way/" target="_blank">PhyloP conservation</A> (WIG format) +<LI> +<A HREF="https://hgdownload.soe.ucsc.edu/goldenPath/geoFor1/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: 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