Reference Code backup Executable files
Fetch chrom.sizes information from UCSC for the given <db>
fetchChromSizes <db> > <db>.chrom.sizes
This tool is part of UCSC Genome Browser's utilities.
fetchChromSizes is a command-line utility commonly used in genomics and bioinformatics to retrieve information about the sizes of chromosomes or scaffolds in a reference genome. If you have the sequence fasta file at hand, you can also use the faidx command from samtools or faSize from UCSC to extract chromosomes' sizes.
This script expects to find one of the following commands: wget, mysql, or ftp in order to fetch information from UCSC.
Route the output to the file .chrom.sizes as indicated above.
The following command will export chromosome sizes for human reference genome (hg38) to a file hg38.chrom.sizes
fetchChromSizes hg38 > hg38.chrom.sizes