bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml index 926b8eb2928..c1caac6714f 100644 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml @@ -683,31 +683,31 @@ <DIV class="otherDb"><span class="types all"></span> <div class="format"><code>otherDb <otherDb></code></div> <P>Track types that show pairwise alignments often need to declare the other species/assembly included in the alignment. Types that use this setting include bed, chain, netAlign, psl and snake.</P> <P><B>Example:</B></P> <pre> otherDb mm10</pre> <P>This example sets the second assembly in the alignment to the mouse mm10 assembly.</P> </DIV> <DIV class="otherTwoBitUrl"><span class="types chain bigChain psl bigPsl"></span> <div class="format"><code>otherTwoBitUrl <url/relativePath></code></div> <P>For pairwise alignment tracks this can specify where to find the query sequence This setting can be used in psl, bigPsl, chain, and bigChain tracks.</P> <P><B>Example:</B></P> - <pre> otherTwoBitUrl https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit</pre> + <pre> otherTwoBitUrl https://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit</pre> </DIV> <DIV class="origAssembly"><span class="types all"></span> <div class="format"><code>origAssembly <db></code></div> <P><I>NOT FOR HUBS.</I></P> <P>The original assembly version for which the dataset was generated. Datasets generated by mapping to one genome assembly may prove useful enough to map to a more recent assembly. Ideally datasets will be regenerated to map to the new assemblies coordinates, but sometimes this is not practical or expedient. Therefore, the dataset may have its genome coordinates "lifted over" to the more recent assembly. In some cases this results in an inferior but nevertheless useful representation. Such datasets should have their original assembly defined with this setting.</P> @@ -2213,31 +2213,31 @@ scores greater than or equal to 900 above will display in black.</P> </DIV> <DIV class="searchIndex"><span class="types bed bigBed"></span> <div class="format"><code>searchIndex <str></code></div> <P> Specifies the list of field names on which a index has been made. When a user enters a string in the position search box of the browser, this index will be searched to find that name, and if the string is in the index, the user will either be navigated to that position in the browser, or if there are more than one matches of that string, will be give a list of the positions to choose from. See <A HREF="../bigBed.html#Ex3">HERE</A> for instructions on how to build an index for a bigBed file. The searchIndex setting requires the input BED data to be case-senstive sorted (<code>sort -k1,1 -k2,2n</code>), where newer versions of the tool bedToBigBed (available - <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">here</a>) + <a href="http://hgdownload.gi.ucsc.edu/admin/exe/">here</a>) are enhanced to catch improper input. <P><B>Example:</B></P> <pre> searchIndex name</pre> </DIV> <DIV class="searchTrix"><span class="types bed bigBed"></span> <div class="format"><code>searchTrix <url/relativePath></code></div> <P> Specifies the URL to a TRIX file that maps free text to a set of indices that are assumed to have indicies in the associated bigBed file. See <a href="../trix.html">here</a> for instructions on how to build a TRIX file and a <a href="../hubQuickStartSearch.html">Searchable Track Hub Quick Start Guide</a> here.</li> <P><B>Example:</B></P> <pre> searchTrix url or relative path </pre> </DIV> @@ -2887,31 +2887,31 @@ with their heights equal to the signal value within the bigWig track. If not sufficiently zoomed in, the bigWig will revert to bars instead of letters by default. See a working example of the <code>logo</code> dynseq display on the <a href="../bigWig.html#Ex4" target="_blank">bigWig</a> help page.</p> <P><B>Example:</B></P> <pre> logo on</pre> </DIV> <DIV class="logoMaf"><span class="types bigWig bigMaf"></span> <div class="format"><code>logoMaf <url/relativePath></code></div> <P>The argument to logoMaf is the path to a MAF alignment (either a table or bigMaf). If set and zoomed into base level, the wiggle will be drawn as a sequence logo calculated by counting the number of each nucleotide aligned to that base, which will be scaled by the value in the wiggle.</p> <P><B>Example:</B></P> - <pre> logoMaf https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz470way/multiz470way.bigMaf</pre> + <pre> logoMaf https://hgdownload.gi.ucsc.edu/goldenPath/hg38/multiz470way/multiz470way.bigMaf</pre> </DIV> <DIV class="mouseOverFunction"><span class="types wig bigWig bedGraph"></span> <div class="format"><code>mouseOverFunction <noAverage></code></div> <P>Limit mouse over value display to only display the fundamental values without any averaging of multiple data points. Display will show "zoom in to see values" when fundamental individual values can not be shown. Useful for tracks where averaging values together is not a valid operation.</P> <P><B>Example:</B></P> <pre> mouseOverFunction noAverage</pre> </DIV> <DIV class="viewLimits"><span class="types wig bigWig bedGraph"></span> <div class="format"> @@ -4261,31 +4261,31 @@ groupings sestanBrainAtlasGroups ... </pre> <P>This microarray dataset refers to groupings defined in the "<code>gnfHumanAtlas2Groups</code>" stanza of the makeDb/hgCgiData/Human/microarrayGroups.ra file. </P> </DIV> <DIV class="extraDetailsTable"><span class="types bigBed"></span> <div class="format"><code>extraDetailsTable <url/relativePath></code></div> <p>This setting was renamed June 2022. Please use <a href="#detailsStaticTable">detailsStaticTable</a> instead.</p> <p> Provides a template to a tab separated text file where $<fieldName> strings will be substituted for data in the bigBed and displayed as an HTML table. For an example of this, please see the following text file: - <a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/gnomAD/v3.1/variants/v3.1.genomes.popTable.txt">http://hgdownload.soe.ucsc.edu/gbdb/hg38/gnomAD/v3.1/variants/v3.1.genomes.popTable.txt</a>, where + <a href="http://hgdownload.gi.ucsc.edu/gbdb/hg38/gnomAD/v3.1/variants/v3.1.genomes.popTable.txt">http://hgdownload.gi.ucsc.edu/gbdb/hg38/gnomAD/v3.1/variants/v3.1.genomes.popTable.txt</a>, where the strings such as "${AC_afr}" will be substituted for the data in that field for the particular item from the bigBed. </p> <p> Note that the same size table is displayed for every item of the bigBed, even if there is missing data in that field for a particular item. For variable size tables, please see <a href="#detailsDynamicTable">detailsDynamicTable</a>. </p> </DIV> <DIV class="extraTableFields"><span class="types bigBed"></span> <div class="format"><code>extraTableFields <fieldName1|table title,fieldName2|table title,...></code></div> <p>This setting was renamed June 2022. Please use <a href="#detailsDynamicTable">detailsDynamicTable</a> instead.</p> <p> Tells the system that the data in <fieldName1,...> contains an <em>encoded</em> table @@ -4345,31 +4345,31 @@ <table class='jsonTable'> <tr><td>annot3</td><td>val3</td></tr> </table> </td> </tr> </table></td></tr> </table> </p> </DIV> <DIV class="detailsStaticTable"><span class="types bigBed"></span> <div class="format"><code>detailsStaticTable <url/relativePath></code></div> <p> Provides a template to a tab separated text file where $<fieldName> strings will be substituted for data in the bigBed and displayed as an HTML table. For an example of this, please see the following text file: - <a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/gnomAD/v3.1/variants/v3.1.genomes.popTable.txt">http://hgdownload.soe.ucsc.edu/gbdb/hg38/gnomAD/v3.1/variants/v3.1.genomes.popTable.txt</a>, where + <a href="http://hgdownload.gi.ucsc.edu/gbdb/hg38/gnomAD/v3.1/variants/v3.1.genomes.popTable.txt">http://hgdownload.gi.ucsc.edu/gbdb/hg38/gnomAD/v3.1/variants/v3.1.genomes.popTable.txt</a>, where the strings such as "${AC_afr}" will be substituted for the data in that field for the particular item from the bigBed. </p> <p> Note that the same size table is displayed for every item of the bigBed, even if there is missing data in that field for a particular item. For variable size tables, please see <a href="#detailsDynamicTable">detailsDynamicTable</a>. </p> </DIV> <DIV class="detailsDynamicTable"><span class="types bigBed"></span> <div class="format"><code>detailsDynamicTable <fieldName1|table title,fieldName2|table title,...></code></div> <p> Tells the system that the data in <fieldName1,...> contains an <em>encoded</em> table that should be turned into a standard HTML table on the details page for that item. If @@ -6594,59 +6594,59 @@ sortOrder cell=+ view=+ type bed 3 html TrackDescription.html track myViewPeaks parent myMultiViewComposite shortLabel Peaks view PK visibility pack type bigBed 12 + track myFirstPeakSubtrack parent myViewPeaks on shortLabel Peak One longLabel Peak One Long - bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/ENCODE4/TFrPeakClusters.bb + bigDataUrl https://hgdownload.gi.ucsc.edu/gbdb/hg38/bbi/ENCODE4/TFrPeakClusters.bb subGroups cell=CD14 view=PK track mySecondPeakSubtrack parent myViewPeaks on shortLabel Peak Two longLabel Peak Two Long - bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/ENCODE4/TFrPeakClusters.bb + bigDataUrl https://hgdownload.gi.ucsc.edu/gbdb/hg38/bbi/ENCODE4/TFrPeakClusters.bb subGroups cell=A1GM12 view=PK track myViewSignals parent myMultiViewComposite shortLabel Peaks view SIG visibility pack type bigWig track myFirstSignalsSubtrack parent myViewSignals on shortLabel Sig One longLabel Sig One Long - bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/wgEncodeRegDnase/wgEncodeRegDnaseUwK562Signal.bw + bigDataUrl https://hgdownload.gi.ucsc.edu/gbdb/hg38/bbi/wgEncodeRegDnase/wgEncodeRegDnaseUwK562Signal.bw subGroups cell=CD14 view=SIG track mySecondSignalsSubtrack parent myViewSignals on shortLabel Sig Two longLabel Sig Two Long - bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/wgEncodeRegDnase/wgEncodeRegDnaseUwK562Signal.bw + bigDataUrl https://hgdownload.gi.ucsc.edu/gbdb/hg38/bbi/wgEncodeRegDnase/wgEncodeRegDnaseUwK562Signal.bw subGroups cell=A1GM12 view=SIG </pre> <p> Similar to the example above, except this example shows a composite track containing two views, one with bigBeds and one with bigBeds, all inside of a superTrack.</p> </DIV> <!-- - - - - - - - CONTAINER/MULTIWIG/AGGREGATE settings - - - - - - - --> <DIV class="container_intro"> <H3>Aggregate or Overlay Tracks: multiWig</H3> <P>In some instances, data from multiple tracks is so closely related that it makes sense to view it as a single track. The premiere example of this is the signal overlay track (i.e. "<code>multiWig</code>"). Signal overlay tracks display the signal data from several subtracks combined in several different ways, making it