409c64a1121ee70c37a7e5178cf42320d683fdc2 gperez2 Fri Feb 28 14:47:15 2025 -0800 Updating example due to a bug with the '+', refs #17555 diff --git src/hg/htdocs/goldenPath/help/hgGenomeHelp.html src/hg/htdocs/goldenPath/help/hgGenomeHelp.html index 1c6bf766ad1..a651c627cbd 100755 --- src/hg/htdocs/goldenPath/help/hgGenomeHelp.html +++ src/hg/htdocs/goldenPath/help/hgGenomeHelp.html @@ -240,40 +240,40 @@ <a href="#Configure">customize</a> the display.</p> <!-- Example #1 --> <a name="example1"></a> <h3>Example #1 — SNPs on chr22</h3> <p> Follow these steps to display in Genome Graphs all of the highest quality SNPs on chromosome 22 for the hg18 assembly whose predicted functional role is "coding non-synonymous" (where there is a change in the peptide for the allele with respect to the reference assembly). Note that there are no SNPs on the p-arm of chromosome 22.</p> <p> This data set is <a href="#Format">formatted</a> in the "<code>marker value</code>" style. The <code>markers</code> are <strong>dbSNP rsIDs</strong>. The associated <code>value</code> is <strong>+1</strong> if the SNP is on the positive strand, and <strong>-1</strong> if the SNP is on the negative strand. Here are the first ten rows of the data file:</p> -<pre><code>rs1007298 +1 -rs1007863 +1 -rs10154509 +1 -rs10154678 +1 -rs10154785 +1 -rs1018448 +1 -rs10212022 +1 -rs1022478 +1 -rs1042311 +1 -rs1042435 +1 </code></pre> +<pre><code>rs1007298 1 +rs1007863 1 +rs10154509 1 +rs10154678 1 +rs10154785 1 +rs1018448 1 +rs10212022 1 +rs1022478 1 +rs1042311 1 +rs1042435 1 </code></pre> <p> <strong>Step 1. Upload the data into the Genome Graphs tool</strong><br> Copy the entire sample <a href="examples/hgGenome_example1.txt">data set</a> into a text editor and save the file to your computer. This data set is associated with the human assembly: hg18 (Mar. 2006). Be sure to configure the Genome Graphs tool to use the hg18 assembly like so:</p> <pre><code><strong>clade:</strong> Vertebrate <strong>genome:</strong> Human <strong>assembly:</strong> Mar. 2006 </code></pre> <p> <a href="#Upload">Upload</a> the file into the Genome Graphs tool. You can configure each <a href="#Controls">control</a> on the upload page, or just leave them set to their default values. The upload process may take some time, as the program is actually mapping each rsID in the input file to its location(s) in the genome.</p> <p>