bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/bigMaf.html src/hg/htdocs/goldenPath/help/bigMaf.html index 8775d0a625f..6f62e5c5b9c 100755 --- src/hg/htdocs/goldenPath/help/bigMaf.html +++ src/hg/htdocs/goldenPath/help/bigMaf.html @@ -115,52 +115,52 @@ <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 +wget http://hgdownload.gi.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 +<a href="http://hgdownload.gi.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> +<a href="http://hgdownload.gi.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 +<a href="http://hgdownload.gi.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 +<a href="http://hgdownload.gi.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> +<a href="http://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes" +target="_blank">http://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes</a>.</p> <pre><code>mafToBigMaf hg38 chr22_KI270731v1_random.maf stdout | sort -k1,1 -k2,2n > bigMaf.txt bedToBigBed -type=bed3+1 -as=bigMaf.as -tab bigMaf.txt hg38.chrom.sizes bigMaf.bb </code></pre> <p>Note that the hg38 in the mafToBigMaf hg38 command indicates the referenceDb and matches the expected prefix of the primary species' sequence name, for instance hg38 for the hg38.chr22_KI270731v1_random found in the input example chr22_KI270731v1_random.maf file.</p> <p> <strong>Step 6.</strong> Follow the below steps to create the binary indexed mafFrames and mafSummary files to accompany your bigMaf file:</p> <pre><code>genePredSingleCover chr22_KI270731v1_random.gp single.gp genePredToMafFrames hg38 chr22_KI270731v1_random.maf bigMafFrames.txt hg38 single.gp bedToBigBed -type=bed3+8 -as=mafFrames.as -tab bigMafFrames.txt hg38.chrom.sizes bigMafFrames.bb hgLoadMafSummary -minSeqSize=1 -test hg38 bigMafSummary chr22_KI270731v1_random.maf cut -f2- bigMafSummary.tab | sort -k1,1 -k2,2n > bigMafSummary.bed @@ -222,66 +222,66 @@ similar to that which is available for a standard MAF track.</p> <h3 id="example2">Example #2</h3> <p> In this example, you will create a bigMaf file from an existing bigMaf input file, <em>bigMaf.txt</em>, located on the UCSC Genome Browser http server.</p> <ol> <li> Save the bed3+1 example file, <a href="examples/bigMaf.txt"><em>bigMaf.txt</em></a>, to your computer (<em>Step 6</em>, above).</li> <li> Save the autoSql file <a href="examples/bigMaf.as"><em>bigMaf.as</em></a> to your computer (<em>Step 3</em>, above).</li> <li> Download the - <a href="http://hgdownload.soe.ucsc.edu/admin/exe/"><code>bedToBigBed</code> utility</a> + <a href="http://hgdownload.gi.ucsc.edu/admin/exe/"><code>bedToBigBed</code> utility</a> (<em>Step 4</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 5</em>, above).</li> <li> Run the <code>bedToBigBed</code> utility to create a binary indexed MAF file (<em>Step 6</em>, above): <pre><code>bedToBigBed -type=bed3+1 -tab -as=bigMaf.as bigMaf.txt hg38.chrom.sizes bigMaf.bb</code></pre></li> <li> Move the newly created bigMaf file (<em>bigMaf.bb</em>) to a web-accessible location (<em>Step 7</em>, above).</li> <li> Construct a track line that points to the bigMaf file (<em>Step 8</em>, above).</li> <li> Create the custom track on the human assembly hg38 (Dec. 2013), and view it in the Genome Browser (<em>step 9</em>, above).</li> </ol> <h2>Sharing your data with others</h2> <p> If you would like to share your bigMaf 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 bigMaf format</h2> <p> Because bigMaf files are an extension of bigBed files, which are indexed binary files, it can be difficult to extract data from them. UCSC has developed the following programs to assist in working with bigBed formats, available from the -<a href="http://hgdownload.soe.ucsc.edu/admin/exe/">binary utilities directory</a>.</p> +<a href="http://hgdownload.gi.ucsc.edu/admin/exe/">binary utilities directory</a>.</p> <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 the <code>bedClip</code> program -(<a href="http://hgdownload.soe.ucsc.edu/admin/exe/">available here</a>) to remove the problematic +(<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" -->