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/bigChain.html src/hg/htdocs/goldenPath/help/bigChain.html index d1fba62c819..87d767735c4 100755 --- src/hg/htdocs/goldenPath/help/bigChain.html +++ src/hg/htdocs/goldenPath/help/bigChain.html @@ -1,25 +1,25 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser bigChain Track Format" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>bigChain Track Format</h1> <p> -The bigChain format describes a pairwise alignment that allow gaps in both sequences simultaneously, +The bigChain format describes a pairwise alignment that allows gaps in both sequences simultaneously, just as <a href="chain.html">chain</a> files do; however, bigChain files are compressed and indexed as <a href="/goldenPath/help/bigBed.html">bigBeds</a>. Chain files are converted to bigChain files using the program <code>bedToBigBed</code>, run with the <code>-as</code> option to pull in a special <a href="http://www.linuxjournal.com/article/5949" target="_blank">autoSql</a> (<em>.as</em>) file that defines the fields of the bigChain.</p> <p> The bigChain files are in an indexed binary format. The main advantage of this format is that only those portions of the file needed to display a particular region are transferred to the Genome Browser server. Because of this, bigChain files have considerably faster display performance than regular chain files when working with large data sets. The bigChain file remains on your local web-accessible server (http, https or ftp), not on the UCSC server, and only the portion needed for the currently displayed chromosomal position is locally cached as a "sparse file". If you do not have access to a web-accessible server and need hosting space for your bigChain files, please see the <a href="hgTrackHubHelp.html#Hosting">Hosting</a> section of the Track Hub Help documentation.</p> @@ -159,31 +159,31 @@ computer (<em>Step 1</em> in <em>Creating a bigChain track</em>, above).</li> <li> Save the autoSql files <a href="examples/bigChain.as"><em>bigChain.as</em></a> and <a href="examples/bigLink.as"><em>bigLink.as</em></a> to your computer (<em>Step 2</em>, above).</li> <li> Download the <code>bedToBigBed</code> and <code>chainToBigChain</code> <a href="http://hgdownload.gi.ucsc.edu/admin/exe/">utilities</a> (<em>Step 3</em>, above).</li> <li> Save the <a href="hg38.chrom.sizes"><em>hg38.chrom.sizes</em> text file</a> to your computer. This file contains the chrom.sizes for the human hg38 assembly (<em>Step 4</em>, above).</li> <li> Run the utilities in <em>Steps 5-7</em>, above, to create the bigChain and bigLink output files. </li> <li> - Place the newly created bigChain (<em>bigChain.bb</em>) and and bigLink + Place the newly created bigChain (<em>bigChain.bb</em>) and bigLink (<em>bigChain.link.bb</em>) files on a web-accessible server (<em>Step 8</em>).</li> <li> Construct a track line that points to the bigChain file (<em>Step 9</em>, above).</li> <li> Create the custom track on the human assembly hg38 (Dec. 2013), and view it in the Genome Browser (<em>Step 10</em>, above).</li> </ol> <h2>Sharing your data with others</h2> <p> If you would like to share your bigChain 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 bigChain format</h2> <p> @@ -194,21 +194,21 @@ <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.</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 the end of the chromosome. If these are present, run +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.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" -->