bbf9b5788beae5c61fe8a30bc824f4b8985927e9 mspeir Wed Nov 20 10:51:05 2024 -0800 changing bigChain steps to use chainToBigChain rather than hgLoadChain, refs #33972 diff --git src/hg/htdocs/goldenPath/help/bigChain.html src/hg/htdocs/goldenPath/help/bigChain.html index a483962..21b28bc 100755 --- src/hg/htdocs/goldenPath/help/bigChain.html +++ src/hg/htdocs/goldenPath/help/bigChain.html @@ -58,80 +58,74 @@ <h2>Creating a bigChain track</h2> <p> To create a bigChain track, follow these steps:</p> <p> <strong>Step 1.</strong> If you already have a chain file you would like to convert to a bigChain, skip to <em>Step 3</em>. Otherwise download <a href="examples/chr22_KI270731v1_random.hg38.mm10.rbest.chain">this example chain file</a> for the human GRCh38 (hg38) assembly.</p> <p> <strong>Step 2.</strong> Download these autoSql files needed by <code>bedToBigBed</code>: <em><a href="examples/bigChain.as">bigChain.as</a></em> and <em><a href="examples/bigLink.as">bigLink.as</a></em>.</p> <p> <strong>Step 3.</strong> -Download the <code>bedToBigBed</code> and <code>hgLoadChain</code> programs from the UCSC +Download the <code>bedToBigBed</code> and <code>chainToBigChain</code> programs from the UCSC <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">binary utilities directory</a>.</p> <p> <strong>Step 4.</strong> Use the <code>fetchChromSizes</code> script from the <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">same directory</a> to create a <em>chrom.sizes</em> file for the UCSC database with which you are working (e.g., hg38). 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 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>.</p> <p> Here are wget commands to obtain these above files. <pre><code>wget https://genome.ucsc.edu/goldenPath/help/examples/bigChain.as wget https://genome.ucsc.edu/goldenPath/help/examples/bigLink.as wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes wget https://genome.ucsc.edu/goldenPath/help/examples/chr22_KI270731v1_random.hg38.mm10.rbest.chain </code></pre></p> +<p> <strong>Step 5.</strong> -Use the <code>hgLoadChain</code> utility to generate the <em>chain.tab</em> and <em>link.tab</em> -files needed to create the bigChain file:</p> -<pre><code>hgLoadChain -noBin -test hg38 bigChain chr22_KI270731v1_random.hg38.mm10.rbest.chain</code></pre> +Use the <code>chainToBigChain</code> utility to generate the pre-bigChain and pre-bigLink files:</p> +<pre><code>chainToBigChain chr22_KI270731v1_random.hg38.mm10.rbest.chain bigChain.pre bigChain.link.pre</code></pre> <p> <strong>Step 6.</strong> -Create the bigChain file from your input chain file using a combination of <code>sed</code>, -<code>awk</code> and the <code>bedToBigBed</code> utility: -<pre><code>sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}' > chr22_KI270731v1_random.hg38.mm10.rbest.bigChain -bedToBigBed -type=bed6+6 -as=bigChain.as -tab chr22_KI270731v1_random.hg38.mm10.rbest.bigChain hg38.chrom.sizes bigChain.bb</code></pre></p> +Create the bigChain and bigLink files using the <code>bedToBigBed</code> utility: +<pre><code>bedToBigBed -type=bed6+6 -as=bigChain.as -tab bigChain.pre hg38.chrom.sizes bigChain.bb +bedToBigBed -type=bed4+1 -as=bigLink.as -tab bigChain.link.pre hg38.chrom.sizes bigChain.link.bb +</code></pre></p> <p> <strong>Step 7.</strong> -To display your date in the Genome Browser, you must also create a binary indexed link file to -accompany your bigChain file:</p> -<pre><code>awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n > bigChain.bigLink -bedToBigBed -type=bed4+1 -as=bigLink.as -tab bigChain.bigLink hg38.chrom.sizes bigChain.link.bb </code></pre> -<p> -<strong>Step 8.</strong> Move the newly created bigChain (<em>bigChain.bb</em>) and bigLink (<em>bigChain.link.bb</em>) files to a web-accessible http, https or ftp location.</p> <p> -<strong>Step 9.</strong> +<strong>Step 8.</strong> Construct a <a href="hgTracksHelp.html#CustomTracks">custom track</a> using a single <a href="hgTracksHelp.html#TRACK">track line</a>. Note that any of the track attributes listed <a href="customTrack.html#TRACK">here</a> are applicable to tracks of type bigBed. The most basic version of the track line will look something like this:</p> <pre><code>track type=bigChain name="My Big Chain" bigDataUrl=http://myorg.edu/mylab/bigChain.bb linkDataUrl=http://myorg.edu/mylab/bigChain.link.bb </code></pre> <p> -<strong>Step 10.</strong> +<strong>Step 9.</strong> Paste the custom track line into the text box on the <a href="../../cgi-bin/hgCustom">custom track management page</a>.</p> <p> The <code>bedToBigBed</code> program can be run with several additional options. For a full list of the available options, type <code>bedToBigBed</code> (with no arguments) on the command line to display the usage message. </p> <h2>Examples</h2> <h3>Example #1</h3> <p> In this example, you will create a bigChain custom track using an existing bigChain file, <em>bigChain.bb</em>, located on the UCSC Genome Browser http server. This file contains data for the hg38 assembly.</p> <p> To create a custom track using this bigChain file: @@ -156,31 +150,31 @@ track display. Note that the details page displays information about the individual chains, similar to that which is available for a standard chain track.</p> <h3>Example #2</h3> <p> In this example, you will create your own bigChain file from an existing chain input file.</p> <ol> <li> Save <a href="examples/chr22_KI270731v1_random.hg38.mm10.rbest.chain">this chain file</a> to your 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>hgLoadChain</code> + Download the <code>bedToBigBed</code> and <code>chainToBigChain</code> <a href="http://hgdownload.soe.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 (<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>