bd5a22bd0280053152df31eab38a492434229612 brianlee Wed Jun 15 07:35:39 2022 -0700 Removing link to bigRmskAlign.txt as it doesn't exist yet, and static page cronjob check on beta finds 404 here, no RM diff --git src/hg/htdocs/goldenPath/help/bigRmsk.html src/hg/htdocs/goldenPath/help/bigRmsk.html index e33d738..406467b 100755 --- src/hg/htdocs/goldenPath/help/bigRmsk.html +++ src/hg/htdocs/goldenPath/help/bigRmsk.html @@ -108,31 +108,31 @@ <p> To create a bigRmsk track, and its supporting file, follow the below steps. All input files into <code>bedToBigBed</code> must be sorted on the coordinates of the first two columns, <code>sort -k1,1 -k2,2n input.tsv.txt > input.tsv.sorted.txt</code>. To learn about a perl program that can build the tab-separated values (tsv) input bedToBigBed text files from the RepeatMasker output files, contact Robert Hubley: <a href="https://github.com/rmhubley" target="_blank">https://github.com/rmhubley</a>.</p> <p> <strong>Step 1.</strong> If you already have an input file you would like to convert to a bigRmsk, skip to <em>Step 3</em>. Otherwise, download <a href="examples/bigRmsk.txt">this example bigRmsk.txt file</a> for the human GRCh38 (hg38) assembly.</p> <p> <strong>Step 2.</strong> If you would like to include the optional auxilary alignment data <code>bigRmskAlign.bb</code> file, -download this <a href="examples/bigRmskAlign.txt">bigRmskAlign.txt file</a>.</p> +download the bigRmskAlign.txt file.</p> <p> <strong>Step 3.</strong> Download the autoSql file <em><a href="examples/bigRmsk.as">bigRmsk.as</a></em> needed by <code>bedToBigBed</code>. If you have opted to include the optional auxilary alignment data file, bigRmskAlign.bb, with your bigRmsk file, you must also download the autoSql file <a href="examples/bigRmskAlignBed.as">bigRmskAlignBed.as</a>.</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/ wget https://genome.ucsc.edu/goldenPath/help/examples/bigRmsk.txt wget https://genome.ucsc.edu/goldenPath/help/examples/bigRmskAlign.txt wget https://genome.ucsc.edu/goldenPath/help/examples/bigRmsk.as wget https://genome.ucsc.edu/goldenPath/help/examples/bigRmskAlign.as wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes </code></pre>