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Tutorial: Get GC Content from UCSC with perl script (mysql)

Hi All,

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:

http://alrlab.research.pdx.edu/aquificales/scripts/get_gc_content.pl

or like this:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e "select chrom, size from  hg19.chromInfo" > hg19.chrom.sizes

Sincerely,

myql ucsc gc-content perl
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updated by Ram Ram • written by Shicheng Guo Shicheng Guo

The post in the current version seems to be missing a valid question or is incomplete. Can you take a look and amend as needed?

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written by GenoMax GenoMax

I am trying to understand your question. Is it as follows:

How can I find nucleotide composition (GC content and such) of genomic regions from bed file using online tools that do not download the reference fasta file to my server/computer. Preferably using ucsc server for the computation.

I believe you might find public versions of Galaxy as the best way to handle such projects. You can get data to Galaxy (like bed files for particular regions) directly from UCSC (no need to download to your server or computer).

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written by Petr Ponomarenko Petr Ponomarenko

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