ddb902a45def533aa68aa2dc7a7213f7fe3cdbe1 dschmelt Mon Nov 4 16:33:15 2019 -0800 Fixing 9 broken links, some for CR#24420 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 2a390d0..2006028 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -97,31 +97,31 @@ <p> Thanks to David Gorkin and Yanxiao Zhang at the <a target="_blank" href="http://renlab.sdsc.edu/renlab_website//">Ren lab (UCSD/Ludwig Institute for Cancer Research)</a> and Iros Barozzi of the <a target="_blank" href="https://biosciences.lbl.gov/divisions/egsb/">Environmental Genomics and Systems Biology Division</a> at the Lawrence Berkeley National Laboratory for providing this data and assisting with track development at UCSC. We would also like to thank Kate Rosenbloom, Conner Powell and the UCSC Genome Browser team for their efforts on this release. </p> <a name="103119"></a> <h2>Oct. 31, 2019 Locus Reference Genomic (LRG) update for human</h2> <p> We are pleased to announce an update to the Locus Reference Genomic (LRG) regions track for human, (<a href="../../cgi-bin/hgTrackUi?db=hg19&c=chrX&g=lrg" target="_blank">GRCh37/hg19</a>) and -<a href="../../cgi-vin/hgTracksUi?db=hg38&c=chrX&g=lrg" target="_blank">(GRCh38/hg38)</a>. Each LRG +<a href="../../cgi-bin/hgTrackUi?db=hg38&c=chrX&g=lrg" target="_blank">(GRCh38/hg38)</a>. Each LRG record also includes at least one stable transcript on which variants may be reported. These transcripts appear in the LRG Transcripts track in the Gene and Gene Predictions track section.</p> <p> This track was produced at UCSC using <a href="ftp://ftp.ebi.ac.uk/pub/databases/lrgex/" target="_blank">LRG XML files</a>. Thanks to <a href="http://www.lrg-sequence.org/documentation/lrg-collaborators/" target="_blank">LRG collaborators</a> for making these data available. We would also like to thank Angie Hinrichs and Jairo Navarro for creating and releasing these tracks.</p> <a name="102819"></a> <h2>Oct. 28, 2019 gnomAD data now available on human (GRCh38/hg38) assembly</h2> <p> We are pleased to announce the new <a target="_blank" href="../cgi-bin/hgTrackUi?db=hg38&c=chr22&g=gnomadVariants">gnomAD Variants super-track</a> for the Human (GRCh38/hg38) assembly. This super-track currently includes <strong>gnomAD v3</strong> @@ -9296,31 +9296,31 @@ <li> chr6_qbl_hap2 -- an A26-B18-DR3 alternate haplotype assembly of the chromosome 6 MHC region based on sequence data from the QBL library (NT_113892.1, NT_113893.1, NT_113894.1, NT_113895.1, NT_113896.1, NT_113897.1).</li> </ul> <p> See the <a href="http://www.sanger.ac.uk/HGP/Chr6/MHC/" target="_blank">Wellcome Trust Sanger Institute MHC Haplotype Project</a> web site for additional information on the chr6 alternate haplotype assemblies.</p> <p> The Y chromosome in this assembly contains two pseudoautosomal regions (PARs) at chrY:1-2709520 and chrY:57443438-57772954. These sequences were taken from the corresponding regions in the X chromosome and are exact duplications of the X chromosome sequences.</p> <p> For further information on NCBI Build 36.1, see the NCBI -<a href="https://www.ncbi.nlm.nih.gov/genome/guide/human/release_notes.html" +<a href="https://www.ncbi.nlm.nih.gov/mapview/stats/BuildStats.cgi?taxid=9606&build=36&ver=1" target="_blank">Build 36.1 release notes</a>.</p> <p> Bulk downloads of the data are available from the UCSC downloads server via <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18" target="_blank">ftp</a> or <a href="http://hgdownload.soe.ucsc.edu/downloads.html#human" target="_blank">http</a>. We recommend that you use ftp or rsync for downloading large or multiple files.</p> <p> We'd like to thank NCBI and the International Human Genome Sequencing Consortium for furnishing the data, and the entire UCSC Genome Browser staff for contributing to this release. Fan Hsu led the UCSC engineering effort; QA was headed up by Ann Zweig.</p> <a name="030606"></a> <h2>Mar. 6, 2006 Purple Sea Urchin genome assembly available in Genome Browser</h2> <p> The Apr. 2005 release of the Purple Sea Urchin genome (<em>Strongylocentrotus purpuratus</em>) is @@ -9546,31 +9546,31 @@ Many thanks to the Broad Institute of MIT and Harvard, Agencourt Bioscience, and the other institutions who contributed to the sequencing, assembly, and mapping efforts. The canFam2 Genome Browser team included Angie Hinrichs, Jennifer Jackson, and Donna Karolchik. See the <a href="credits.html#dog_credits">credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="121505"></a> <h2>Dec. 15, 2005 New Mouse assembly available in Genome Browser</h2> <p> The latest mouse genome assembly from the Mouse Genome Sequencing Consortium, NCBI Build 35 (UCSC version mm7), is now available in the UCSC Genome Browser.</p> <p> The Build 35 assembly includes approximately 2.6 Gb of sequence, of which about 2.2 Gb is finished sequence. Chromosomes 2, 4, 11 and X are finished in this build. To review in-depth statistics on the assembly, see the NCBI -<a href="https://www.ncbi.nlm.nih.gov/genome/guide/mouse/contig/Build35.html" +<a href="https://www.ncbi.nlm.nih.gov/genome/guide/mouse/release_notes.html" target="_blank">Build 35 Data</a> web page. Please note that the UCSC mm7 database contains only the reference strain C57BL/6J.</p> <p> The mm7 sequence and annotation data may be downloaded from the Genome Browser <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/mm7/">FTP server</a> or <a href="http://hgdownload.soe.ucsc.edu/goldenPath/mm7/">Downloads</a> web page. The mm7 annotation tracks were generated by UCSC and collaborators worldwide.</p> <p> We'd like to thank Deanna Church and the Mouse Genome Sequencing Consortium for this assembly. We'd also like to acknowledge the work of the UCSC mm7 team: Hiram Clawson, Fan Hsu, Ann Zweig, Kayla Smith, Robert Kuhn and Donna Karolchik. For a complete list of the individuals and organizations who participated in this assembly, see the <a href="credits.html#mouse_credits">Credits</a> page.</p> <a name="1202b05"></a> <h2Dec. 2, 2005 Announcing the VisiGene Image Browser</h2> @@ -9913,31 +9913,31 @@ page for a detailed list of the organizations and individuals who contributed to the release of this browser.</p> <a name="050405"></a> <h2>May 5, 2005 New Mouse assembly available in Genome Browser</h2> <p> The latest mouse genome assembly from the Mouse Genome Sequencing Consortium, NCBI Build 34 (UCSC version mm6), is now available in the UCSC Genome Browser. In conjunction with this release, we have archived mouse assemblies mm3 and mm4. All archived assemblies are available for download via our <a href="http://hgdownload.soe.ucsc.edu/downloads.html#mouse" target="_blank">downloads server</a>.</p> <p> The Build 34 assembly has an assembled length of approximately 2.6 Gb, of which about 1.9 Gb is finished sequence. Chromosomes 2, 4, 11 and X are finished in this build. To review in-depth statistics on the assembly, see the NCBI -<a href="https://www.ncbi.nlm.nih.gov/genome/guide/mouse/contig/Build34.html" +<a href="www.ncbi.nlm.nih.gov/genome/guide/mouse/release_notes.html" target="_blank">Build 34 Data</a> web page. NOTE: In the Genome Browser mm6 assembly, chrY_random erroneously contains a region duplicated from chrY. For more information about this issue, see the Genome Browser <a href="../FAQ/FAQdownloads.html#download30">FAQ</a>. Please also note that the UCSC mm6 database contains only the reference strain C57BL/6J.</p> <p> The mm6 sequence and annotation data may be downloaded from the Genome Browser <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/mm6/">FTP server</a> or <a href="http://hgdownload.soe.ucsc.edu/goldenPath/mm6/">Downloads</a> web page. The mm6 annotation tracks were generated by UCSC and collaborators worldwide.</p> <p> Mirror sites, please note: due to the size of the comparative genomics annotations in this assembly, the data set requires an unusually large amount of disk space. If you regularly download updates of the mouse data to your site, you may want to examine your available disk space before adding the annotation database from this assembly and/or reschedule your download for a period of low activity on your server. The size of the mm6 annotation database directory @@ -11207,31 +11207,31 @@ - downloadable data files - updated weekly on Sunday morning<br> - outdated sequences - removed once per quarter<br></p> <p> Mirror sites are not required to migrate to an incremental update process, and should not experience problems as a result of this upgrade. Mirror site questions should be addressed to <a href="mailto:genome-mirror@soe.ucsc.edu">genome-mirror@soe.ucsc.edu</a>. <!-- above address is genome-mirror at soe.ucsc.edu --> <p> We'd like to acknowledge the hard work of Mark Diekhans in the implementation of this new feature, and thank the QA and sysadmin teams (particularly Paul Tatarsky) for their support in this release.</p> <a name="101703a"></a> <h2>Oct. 17, 2003 UCSC Table Browser enhancements</h2> <p> -The UCSC <a href="../cgi-bin/hgText">Table Browser</a> is an excellent tool for retrieving and +The UCSC <a href="../cgi-bin/hgTables">Table Browser</a> is an excellent tool for retrieving and searching the data underlying the Genome Browser. We've recently added some new features to the Table Browser to make it even easier to query and download data.</p> <p> Many of our users have requested a batch query utility that will allow them to paste in or upload a list of terms on which to search. You can now do this by clicking the "Item name/accession" button, then uploading a list of search terms by selecting the "Paste in" or "Upload" option. Note that the Paste option supports wildcards, but the Upload option does not.</p> <p> We've also added 2 new lists of searchable tables/tracks. The Browser tracks list contains the names of annotation tracks in the currently selected assembly as they appear in the Genome Browser. This list is useful if you don't know the name of the underlying database table that contains the data in which you're interested. The Custom tracks list contains the names of all custom annotation tables currently loaded into the Genome Browser for the given assembly. This includes tracks that have been created/loaded by the user as well as custom annotations created via the Table @@ -11586,31 +11586,31 @@ <p> Thanks to everybody at UCSC and around the world that contributed to this release!</p> <h2>Feb. 5, 2003 Enhanced version of Genome Browser released</h2> <p> We're proud to announce the release of version 17 of the UCSC Genome Browser. This version contains powerful new features, numerous improvements to the annotation track display, additional annotation tracks, and a number of bug fixes. In this release cycle, we've also introduced an enhanced QA process that formalizes our testing and verification of the Genome Browser software and the data displayed in the browser.</p> <p> <strong>New functionality in v.17:</strong><br> -- Numerous enhancements to the table browser that allow the user to conduct more complex and specific searches. New features include support for intersections of tracks, a new summary statistics output format, and the ability to output query results as a custom annotation track that -can be viewed in the Genome Browser. The new <a href="help/hgTextHelp.html" target="_blank">Table +can be viewed in the Genome Browser. The new <a href="help/hgTablesHelp.html" target="_blank">Table Browser User's Guide</a> contains a detailed description of the new features and provides a wealth of information and examples for conducting various types of searches on the database tables.</p> <p> -- Two new display modes available for most annotation tracks: pack and squish modes. In <em>pack mode</em> display, annotation track features are fully displayed, but more than one feature may be displayed on the same line. This greatly reduces the amount of display space needed by a track when a user wishes to view a large number of individual features at one time. <em>Squish mode</em> is similar to pack mode, but displays features at 50% height and without labels. This mode is particularly useful for viewing tracks in which a large number of features align to the same section of a chromosome, e.g. EST tracks.</p> <p> -- Functional groupings of annotation track controls. This makes it much easier to find a particular item in the track control list and gives a better visual overview of the annotations available in a particular category, e.g. comparative genomics tracks or gene prediction tracks.</p> <p> @@ -11831,31 +11831,31 @@ Bulk downloads of the Jun. 2002 Build 30 human genome assembly (hg12) are now available from the <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg12/" target="_blank">downloads server</a>. This initial release of the annotation database download contains a limited set of tables. Additional files will be available for download next week.</p> <h2>Jul. 24, 2002 Human assembly hg12 blat server available</h2> <p> The BLAT server and the coordinates conversion feature for human genome assembly Build 30 (hg12) are now functional.</p> <h2>Jul. 23, 2002 Pre-release of human draft assembly Build 30 in Genome Browser</h2> <p> We're pleased to announce the pre-release of a browser for human genome assembly Build 30 from NCBI (UCSC version hg12). This assembly was produced at NCBI based on sequence information submitted into GenBank as of Jun. 28, 2002. Build 30 release notes and statistics will soon be available from the -<a href="https://www.ncbi.nlm.nih.gov/genome/guide/human/" target="_blank">NCBI web site</a>.</p> +<a href="https://www.ncbi.nlm.nih.gov/" target="_blank">NCBI web site</a>.</p> <p> Build 30 is an excellent high-quality assembly. It contains nearly 87% finished sequence, and 94%-97% coverage. The sequence coverage of this build is much higher than in previous releases, and there is a high level of correspondence between the sequence and the map. Currently, the human genome project appears to be on track to achieve the goal of finishing at least 95% of the human genome (using Bermuda standards) by Apr. 2003.</p> <p> UCSC has generated a set of high-level comparisons of the Build 30 draft sequence against various types of information (STS maps, BAC end pairs, and clone overlaps), accessible from the <a href="http://hgdownload.soe.ucsc.edu/goldenPath/human/chromReports/24Jun2002/" target="_blank">Chromosome Reports</a> and <a href="http://hgdownload.soe.ucsc.edu/goldenPath/human/mapPlots/" target="_blank">Genome Map Plots</a> links in the "Technical Information about the Assembled Sequence" section below.</p> <p> @@ -11898,33 +11898,31 @@ This release also includes an updated <a href="help/hgTracksHelp.html" target="_blank">User's Guide</a> and more detailed documentation on creating & using <a href="help/customTrack.html" target="_blank">custom annotation tracks</a>.</p> <h2>May 24, 2002 Bulk data downloads for human assembly hg11 now available</h2> <p> Bulk downloads of the April 2002 hg11 human genome assembly (NCBI Build 29) are now available from the <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg11/" target="_blank">downloads server</a>.</p> <h2>May 22, 2002 Human draft assembly Build 29 released in Genome Browser</h2> <p> We've just released a browser and BLAT server on the latest Build 29 human genome assembly from NCBI (UCSC version hg11). This assembly is based on sequence information submitted into GenBank as of Apr. 5 2002. As with the Dec. 2001 (hg10) release, this assembly was produced at NCBI rather than at -UCSC. Consult NCBI's <a href="https://www.ncbi.nlm.nih.gov/genome/guide/human/release_notes.html" -target="_blank">Build 29 release notes</a> and -<a href="https://www.ncbi.nlm.nih.gov/genome/guide/human/HsStats.html" target="_blank">statistics</a> +UCSC. Consult NCBI's Build 29 release notes and statistics for more information about this release. This assembly contains nearly 75% finished sequence. Currently, the human genome project appears to be on track to achieve the goal of finishing at least 95% of the human genome (using Bermuda standards) by Apr. 2003.</p> <p> Although the NCBI human genome assembly has been steadily improving over the past year, mapping problems still exist in the current release. Most are small, relatively local rearrangements. Larger scale problems include a rearrangement in the p-arm of Chr16 and several discrepancies in Chr17. Researchers - especially positional cloners - are strongly encouraged to use the tools provided (<a href="http://hgdownload.soe.ucsc.edu/goldenPath/human/mapPlots/" target="_blank">comparison plots</a>, <a href="http://hgdownload.soe.ucsc.edu/goldenPath/human/chromReports/" target="_blank">chromosome reports</a>) to evaluate the accuracy of the assembly in specific regions of interest.</p> <p> Bulk downloads of the hg11 data should be available from this site in approximately one week. New annotation tracks will be posted as soon as they become available.</p>