[BioC] GC counts

[Steve Lianoglou]

Hi Catarina,

On Sat, Sep 28, 2013 at 3:59 AM, Catarina [guest]
<guest at bioconductor.org> wrote:
>
> Hi!
>
> I'm very new to genetic and I'm afraid I have the most basic question. Why do you normalize for GC counts and not for AT counts? I know that GC establishes 3 hydrogen bounds and AT only two. The stronger the bound, the easier to determine where it is/how many there are? Is this ti?

Can you be more specific? Can you provide the context of the
normalization you are talking about? I mean, is there a particular
assay you are working with (PCR? next gen seq? microarray?) that
you've found a "normalization" required for GC content?

You will find a lot of (general and specific) information on this
topic if you simply google for "gc bias".

If that is not sufficient, please ask a more specific question as it
relates to the (bioinformatics) problem you are  trying to solve.

HTH,

-steve

-- 
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech