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 *.align files from RepeatMasker, the track will function with reduced functionality without them. Just skip the steps involved in build the alignment files.
Step 2. Download the autoSql schemes bigRmskBed.as and bigRmskAlignBed.as:
wget https://genome.ucsc.edu/goldenPath/help/examples/bigRmskBed.as
wget https://genome.ucsc.edu/goldenPath/help/examples/bigRmskAlignBed.as
You will also need a file of chromosome sizes for your genome, or download the hg38 file for the example:
- wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes+ wget http://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes
Step 3. Convert the RepeatMasker files to the text format bigRmsk files for conversion to the bigRmsk files with rmToTrackHub.pl, which sorts the output for direct input to bedToBigBed:
RepeatMasker/util/rmToTrackHub.pl -out bigRmskExample.out -align bigRmskExample.align
Step 4. Build the bigRmsk and optional bigRmskAlign files:
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
Step 6.