[Genome] Determining nucleotide composition in genomic sections

[Archana Thakkapallayil]

Hello Celina,

There is a program available in the Genome Browser source code called 
'faCount' that you can use to count base statistics and CpGs in FA files. 

The source code is freely available for academic, non-profit and 
personal use from here:

http://genome.ucsc.edu/FAQ/FAQlicense#license3

faCount is in the directory: src/utils/faCount/.

You can obtain the source tree either via CVS:
    http://genome.ucsc.edu/admin/cvs.html
or a zip file:
    http://hgdownload.cse.ucsc.edu/admin/jksrc.zip

Please note the build instructions:
    http://genome.ucsc.edu/admin/jk-install.html

All of the kent utilities output their usage message and command line 
options by running them with no arguments.

I hope this is helpful to you.  Please don't hesitate to contact us 
again if you require further assistance.

Regards,

Archana
UCSC Genome Bioinformatics Group

Montemayor, Celina wrote:
> Hi,
>  
> I was wondering if there's a way of determining the amount (or percentage) of As, Ts, Cs, and Gs within particular genomic sections (i,e, within one of my BED files)? or at least determine the total amount of As, Ts, Cs, and Gs in a specific genome?
>  
> Thank you very much,
>  
> Celina Montemayor
> Graduate Student, Pereira lab
> Baylor College of Medicine
> Houston, Texas
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