198c9b8daecc44fbda6a6494c566c723920f030a lrnassar Wed Mar 11 18:25:21 2026 -0700 Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM. diff --git src/hg/htdocs/goldenPath/help/bigBed.html src/hg/htdocs/goldenPath/help/bigBed.html index e3b907599a8..7d871b80c00 100755 --- src/hg/htdocs/goldenPath/help/bigBed.html +++ src/hg/htdocs/goldenPath/help/bigBed.html @@ -263,46 +263,46 @@ <code>-as=bedExample2.as</code> to help correctly interpret all the columns in the data. </p> <p> This example also demonstrates how to create an extra search index on the name field, and the first of the extra fields to be used for track item search. The searchIndex setting requires the input BED data to be case-sensitive sorted (<code>sort -k1,1 -k2,2n</code>), where newer versions of the tool bedToBigBed (available <a href="http://hgdownload.gi.ucsc.edu/admin/exe/">here</a>) are enhanced to catch improper input.</p> <ol> <li> Save the BED file <a href="examples/bedExample2.bed"><em>bedExample2.bed</em></a> to your computer (<em>Steps 1</em> and <em>2</em> in <em>Creating a bigBed track</em>, above).</li> <li> Save the file <a href="hg18.chrom.sizes"><em>hg18.chrom.sizes</em></a> to your computer. This file - contains the chrom.sizes for the human (hg18) assembly (<em>Step 4</em>, above).</li> + contains the chrom.sizes for the human (hg18) assembly (<em>Step 3</em>, above).</li> <li> Save the AutoSql file <a href="examples/bedExample2.as"><em>bedExample2.as</em></a> to your computer. This file contains descriptions of the BED fields, and is required when the BED file contains a <em>color</em> field.</li> <li> - Download the <code>bedToBigBed</code> utility (<em>Step 3</em>, above).</li> + Download the <code>bedToBigBed</code> utility (<em>Step 2</em>, above).</li> <li> Run the utility to create a bigBed output file with an index on the name field and the first - extra field: (<em>Step 5</em>, above): + extra field: (<em>Step 4</em>, above): <pre><code>bedToBigBed -as=bedExample2.as -type=bed9+2 -extraIndex=name,geneSymbol bedExample2.bed hg18.chrom.sizes myBigBed2.bb</code></pre></li> Place the bigBed file you just created (<em>myBigBed2.bb</em>) on a web-accessible server - (<em>Step 6</em>, above).</li> + (<em>Step 5</em>, above).</li> <li> Paste the URL of the file into the custom tracks entry form, or alternatively construct a track - line that points to your bigBed file (<em>Step 7</em>, above). Because this bigBed file includes a + line that points to your bigBed file (<em>Step 6</em>, above). Because this bigBed file includes a field for color, you must include the <a href="../../FAQ/FAQformat.html#format1"><code>itemRgb</code></a> attribute in the track line. It will look somewhat similar to this (note that you must insert the URL specific to your own bigBed file): <pre><code>track type=bigBed name="bigBed Example Three" description="A bigBed File with Color and two Extra Fields" itemRgb="On" bigDataUrl=http://yourWebAddress/myBigBed2.bb</code></pre></li> <li> Create the custom track on the human assembly hg18 (Mar. 2006), and view it in the Genome Browser (<em>step 8</em>, above). Note that the original BED file contains data on chromosome 7 only.</li> <li> If you are using the bigBed file in a track hub, you can use the additional indices for track item searches. See the setting "searchIndex" in the <a href="trackDb/trackDbHub.html#searchIndex">Track Database Definition Document</a> for more information. For example, if you run the <code>bedToBigBed</code> utility with the option <code>-extraIndex=name</code>, you will be able to search on the "name" field by adding the line <code>searchIndex name</code> to the stanza about your bigBed in the hub's