bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/bigRmsk.html src/hg/htdocs/goldenPath/help/bigRmsk.html index 497a48f3d58..8b07634d683 100755 --- src/hg/htdocs/goldenPath/help/bigRmsk.html +++ src/hg/htdocs/goldenPath/help/bigRmsk.html @@ -218,31 +218,31 @@ Generating the alignment bigRmsk file is optional if you don't have the <em>*.align</em> files from RepeatMasker, the track will function with reduced functionality without them. Just skip the steps involved in build the alignment files. <p> <strong>Step 2.</strong> Download the autoSql schemes <a href="examples/bigRmskBed.as">bigRmskBed.as</a> and <a href="examples/bigRmskAlignBed.as">bigRmskAlignBed.as</a>: <pre> wget https://genome.ucsc.edu/goldenPath/help/examples/bigRmskBed.as wget https://genome.ucsc.edu/goldenPath/help/examples/bigRmskAlignBed.as</pre> <p> You will also need a file of chromosome sizes for your genome, or download the hg38 file for the example: <pre> - wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes</pre> + wget http://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes</pre> <p> <strong>Step 3.</strong> Convert the RepeatMasker files to the text format bigRmsk files for conversion to the bigRmsk files with <em>rmToTrackHub.pl</em>, which sorts the output for direct input to <em>bedToBigBed</em>: <pre> RepeatMasker/util/rmToTrackHub.pl -out bigRmskExample.out -align bigRmskExample.align</pre> <p> <strong>Step 4.</strong> Build the bigRmsk and optional bigRmskAlign files: <pre> bedToBigBed -tab -type=bed9+5 -as=bigRmskBed.as bigRmskExample.join.tsv hg38.chrom.sizes bigRmskExample.bb bedToBigBed -tab -type=bed3+14 -as=bigRmskAlignBed.as bigRmskExample.align.tsv hg38.chrom.sizes bigRmskExampleAlign.bb</pre> <p> <strong>Step 6.</strong>