bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/barChart.html src/hg/htdocs/goldenPath/help/barChart.html index 0a881120a18..bd4d3074a39 100755 --- src/hg/htdocs/goldenPath/help/barChart.html +++ src/hg/htdocs/goldenPath/help/barChart.html @@ -231,31 +231,31 @@ along with the rest of this example. <p> To create a custom track in this form, follow the below steps: <ol> <li>Create a bed6+1 file to use as a map for the items in your matrix (does not need to be all-inclusive). This file, with example lines such as: <pre><code> chr14 95086227 95158010 ENSG00000100697.10 999 - DICER1 </code></pre> will be one of three input files to the helper script expMatrixToBarchartBed. For an example file to follow along with the rest of this example, you can download an example bed6+1 file <a href="examples/barChart/hg38.gtexTranscripts">here</a>.</li> <li>Download the helper programs <em>expMatrixToBarchartBed</em> and <em>bedJoinTabOffset</em> - from the <a href="http://hgdownload.soe.ucsc.edu/admin/exe">utilities directory</a> + from the <a href="http://hgdownload.gi.ucsc.edu/admin/exe">utilities directory</a> appropriate for your operating system. </li> <li>Make sure the programs downloaded above are in your system's PATH variable. For example, if you downloaded the programs to your $HOME/Downloads directory, set your PATH variable accordingly: <pre><code> export PATH=$PATH:$HOME/Downloads </code></pre></li> <li>Now run <em>expMatrixToBarchartBed</em> (which in turn runs <em>bedJoinTabOffset</em>) like so: <pre><code> expMatrixToBarchartBed categoriesFile matrixFile bedInputFile outputBed </code></pre> The argument outputBed will be a bed6+5 file, with the expCount, expScores, _dataOffset, and _dataLen fields computed for you, for example: <pre><code> chr14 95086227 95158010 ENSG00000100697.10 999 - DICER1 5 10.94,11.60,8.00,6.69,4.89 93153 26789 @@ -295,40 +295,40 @@ <em>expMatrixToBarchartBed</em> or <em>bedJoinTabOffset</em>, run the program with no arguments to get a usage message. </p> <a name="example4"></a> <h6>Example #4</h6> <p> In this example, you will use the bed6+5 file created in Example 3 to create a bigBarChart file, allowing the data to be remotely accessed and exist within a track hub. The track settings for bigBarChart on a hub can be viewed <a href="./trackDb/trackDbHub.html#bigBarChart">here</a>. </p> <ol> <li>If not already completed, follow steps 1-4 from <a href="#example3">Example 3</a> above, or download the example bed6+5 file <a href="examples/barChart/hg38.gtexTranscripts.bed">here</a> </li> <li>Download the <em>fetchChromSizes</em> and <em>bedToBigBed</em> programs from the - <a href="http://hgdownload.soe.ucsc.edu/admin/exe">utilities directory</a> appropriate to your + <a href="http://hgdownload.gi.ucsc.edu/admin/exe">utilities directory</a> appropriate to your operating system. <li>Use <em>fetchChromSizes</em> to create a <em>chrom.sizes</em> file for the UCSC database you are working with (hg38 for these examples). Alternatively, you can download the <em>chrom.sizes</em> file for any assembly hosted at UCSC from - our <a href="http://hgdownload.soe.ucsc.edu/downloads.html">downloads</a> page (click on "Full + our <a href="http://hgdownload.gi.ucsc.edu/downloads.html">downloads</a> page (click on "Full data set" for any assembly). For example, the <em>hg38.chrom.sizes</em> file for the hg38 database is located at - <a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes" - target="_blank">http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes</a>.</li> + <a href="http://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes" + target="_blank">http://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes</a>.</li> <li>Save the autoSql file <a href="examples/barChart/barChartBed.as">barChartBed.as</a> to your computer.</li> <li>Run bedToBigBed to create the bigBarChart file: <pre><code> bedToBigBed -as=barChartBed.as -type=bed6+5 inputBed hg38.chrom.sizes output.bigBed </code></pre></li> <li>Move the newly constructed bigBarChart file to a web accessible http, https, or ftp location.</li> <li>Construct a custom track line with a bigDataUrl parameter pointing to the newly created bigBarChart file. If the matrix and category files used to make the precursor barChart file are also moved to an http, https, or ftp location, we can point to them on the custom track line as well (all settings must be on the same line): <pre><code> track type=bigBarChart name="bigBarChart Example One" description="A bigBarChart file" barChartBars="adiposeSubcut breastMamTissue colonTransverse muscleSkeletal wholeBlood" barChartMetric=median barChartUnit=RPKM bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/barChart/hg38.gtexTranscripts.bb @@ -409,31 +409,31 @@ collections based on metadata.</p> <p>The setting <code>barChartFacets <column1,column2,...columnN></code> turns on the faceted selection on the track details and configure page which is useful for selecting which bars out of a large number to display by clicking designated checkboxes. The setting <code>barChartStatsUrl <url></code> associates a table in tab-separated values with the barChart, with one line per bar. And the setting <code>barChartMerge on</code> enables a merge button inside of the faceted selections. It is particularly useful when there are many bars and many facets to condense a related group, such as tissue source.</p> <p> Below is an example track using these settings on source data for a <a href="/cgi-bin/hgTracks?db=hg38&hideTracks=1&tabulaSapiensTissueCellType=pack&tabulaSapiens=show" target="_blank">Tabula Sapiens single cell RNA data from many tissues</a> track. This excerpt of settings from that track allows experimenting to see these settings in action, and to be loaded by going to the My Data, Custom Tracks page.</p> <pre> -track type=bigBarChart name="ex Tabula Sapiens" description="A bigBarChart using Tabula Sapiens data to illustrate new Details pages" visibility=pack barChartCategoryUrl=http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/tabulaSapiens/bw_edit_tissue_cell_type.categories barChartFacets=tissue,cell_class,cell_type barChartStatsUrl=http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/tabulaSapiens/bw_edit_tissue_cell_type.facets barChartMerge=on bigDataUrl=http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/tabulaSapiens/tissue_cell_type.bb +track type=bigBarChart name="ex Tabula Sapiens" description="A bigBarChart using Tabula Sapiens data to illustrate new Details pages" visibility=pack barChartCategoryUrl=http://hgdownload.gi.ucsc.edu/gbdb/hg38/bbi/tabulaSapiens/bw_edit_tissue_cell_type.categories barChartFacets=tissue,cell_class,cell_type barChartStatsUrl=http://hgdownload.gi.ucsc.edu/gbdb/hg38/bbi/tabulaSapiens/bw_edit_tissue_cell_type.facets barChartMerge=on bigDataUrl=http://hgdownload.gi.ucsc.edu/gbdb/hg38/bbi/tabulaSapiens/tissue_cell_type.bb </pre> <p> Once loaded, click into an item to see the details page, in this case for the gene ACE2 at the default position in hg38. On the details page, rather than a static bar chart image, there is a dynamic interactive selection screen with checkbox facets to narrow down the display. Adding <code>barChartMerge on</code> enables the display of the "merge" button, and <code>barChartFacets tissue,cell_class,cell_type</code> sources information in <code>barChartStatsUrl ...tissue_cell_type.facets</code> to enable the facet options. To interact with this example, click the first two "merge" buttons next to "tissue" and "cell_class."</p> <div class="text-center"> <img src="../../images/barChartFacets1.png" alt="Example1 of Facets on barCharts" width="700"> </div> <p> With those two merged selections, then click on the "Macrophage" option to see just @@ -552,37 +552,37 @@ </p> <pre> track name="My singleCell barChart" type=bigBarChart bigDataUrl=https://hgwdev.gi.ucsc.edu/goldenPath/help/examples/barChart/singleCell/myTissueComp.bb </pre> --> <h2>Sharing your data with others</h2> <p> If you would like to share your barChart/bigBarChart data track with a colleague, learn how to create a URL by looking at Example 6 on <a href="customTrack.html#EXAMPLE6">this page</a>.</p> <h2>Extracting data from the bigBarChart format</h2> <p> Because bigBarChart files are an extension of bigBed files, which are indexed binary files, it can be difficult to extract data from them. UCSC has developed the following programs to assist in working with bigBed formats, available from the -<a href="http://hgdownload.soe.ucsc.edu/admin/exe/">binary utilities directory</a>.</p> +<a href="http://hgdownload.gi.ucsc.edu/admin/exe/">binary utilities directory</a>.</p> <ul> <li> <code>bigBedToBed</code> — converts a bigBed file to ASCII BED format.</li> <li> <code>bigBedSummary</code> — extracts summary information from a bigBed file.</li> <li> <code>bigBedInfo</code> — prints out information about a bigBed file. Use the -as option to see the file field descriptions.</li> </ul> <p> As with all UCSC Genome Browser programs, simply type the program name (with no parameters) at the command line to view the usage statement.</p> <h2>Troubleshooting</h2> <p> If you encounter an error when you run the <code>bedToBigBed</code> program, check your input file for data coordinates that extend past the end of the chromosome. If these are present, run the <code>bedClip</code> program -(<a href="http://hgdownload.soe.ucsc.edu/admin/exe/">available here</a>) to remove the problematic +(<a href="http://hgdownload.gi.ucsc.edu/admin/exe/">available here</a>) to remove the problematic row(s) in your input file before running the <code>bedToBigBed</code> program.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->