I have a bed file contents hundred of human genomic regions. I want to get some basic characteristics for these genomic regions, like GC contents et.c. Any perl script could do it without download the fastq files for these regions.
I know if you download the fasta files for these regions, you can use the following script to calculate GC contents:
or like this:
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e "select chrom, size from hg19.chromInfo" > hg19.chrom.sizes