b6b83e88048180ae13593ec462986145bb27a12b brianlee Wed Feb 17 10:16:04 2021 -0800 Adding some simple wget commands to make example process eaiser in bigMaf refs #27009 diff --git src/hg/htdocs/goldenPath/help/bigMaf.html src/hg/htdocs/goldenPath/help/bigMaf.html index d097144..c084221 100755 --- src/hg/htdocs/goldenPath/help/bigMaf.html +++ src/hg/htdocs/goldenPath/help/bigMaf.html @@ -52,30 +52,39 @@ If you already have a MAF file you would like to convert to a bigMaf, skip to <em>Step 3</em>. Otherwise, download <a href="examples/chr22_KI270731v1_random.maf">this example MAF file</a> for the human GRCh38 (hg38) assembly.</p> <p> <strong>Step 2.</strong> If you would like to include optional reading frame and block summary information, download the <a href="examples/chr22_KI270731v1_random.gp">chr22_KI270731v1_random.gp</a> genePred file.</p> <p> <strong>Step 3.</strong> Download the autoSql file <em><a href="examples/bigMaf.as">bigMaf.as</a></em> needed by <code>bedToBigBed</code>. If you have opted to include the optional frame summary and information with your bigMaf file, you must also download the autoSql files <a href="examples/mafSummary.as">mafSummary.as</a> and <a href="examples/mafFrames.as">mafFrames.as</a> files.</p> <p> +Here are wget commands to obtain the above files and the hg38.chrom.sizes file mentioned below: +<pre><code>wget https://genome.ucsc.edu/goldenPath/help/examples/chr22_KI270731v1_random.maf +wget https://genome.ucsc.edu/goldenPath/help/examples/chr22_KI270731v1_random.gp +wget https://genome.ucsc.edu/goldenPath/help/examples/bigMaf.as +wget https://genome.ucsc.edu/goldenPath/help/examples/mafSummary.as +wget https://genome.ucsc.edu/goldenPath/help/examples/mafFrames.as +wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes +</code></pre> +<p> <strong>Step 4.</strong> Download the <code>bedToBigBed</code> and <code>mafToBigMaf</code> programs from the UCSC <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">binary utilities directory</a>. If you have opted to generate the optional frame and summary files for your multiple alignment, you must also download the <code>hgLoadMafSummary</code>, <code>genePredSingleCover</code>, and <code>genePredToMafFrames</code> programs from the same <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">directory</a>.</p> <p> <strong>Step 5.</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 @@ -99,31 +108,31 @@ <p> <strong>Step 7.</strong> Move the newly created bigMaf file (<em>bigMaf.bb</em>) to a web-accessible http, https or ftp location. If you generated the <em>bigMafSummary.bb</em> and/or <em>bigMafFrames.bb</em> files, move those to a web accessible location, likely same location as the <em>bigMaf.bb</em> file.</p> <p> <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=bigMaf name="My Big MAF" description="A Multiple Alignment" bigDataUrl=http://myorg.edu/mylab/bigMaf.bb</code></pre> <p> <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> +management page</a>. Navigate to chr22_KI270731v1_random to see the example data for this track.</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 bigMaf custom track using an existing bigMaf file, <em>bigMaf.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 bigMaf file: <ol>