To create a bigRmsk track, and its supporting file, follow the below steps. All input
files into bedToBigBed must be sorted on the coordinates of the first two columns,
sort -k1,1 -k2,2n input.tsv.txt > input.tsv.sorted.txt. 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: https://github.com/rmhubley.
Step 1. If you already have an input file you would like to convert to a bigRmsk, skip to Step 3. Otherwise, download this example bigRmsk.txt file for the human GRCh38 (hg38) assembly.
Step 2.
If you would like to include the optional auxilary alignment data bigRmskAlign.bb file,
-download this bigRmskAlign.txt file.
Step 3.
Download the autoSql file bigRmsk.as needed by
bedToBigBed. 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
bigRmskAlignBed.as.
Here are wget commands to obtain the above files and the hg38.chrom.sizes file mentioned below:
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