GC counts
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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? Thanks in advance! Catarina -- output of sessionInfo(): - -- Sent via the guest posting facility at bioconductor.org.
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@steve-lianoglou-2771
Last seen 13 months ago
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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
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FYI, this ended up getting discussed on biostars (http://www.biostars.org/p/82308/) and the context turned out to be RNAseq normalization (the question ended up being answered there as well). ____________________________________________ Devon Ryan, Ph.D. Email: dpryan at dpryan.com Tel: +49 (0)178 298-6067 Molecular and Cellular Cognition Lab German Centre for Neurodegenerative Diseases (DZNE) Ludwig-Erhard-Allee 2 53175 Bonn, Germany On Sep 30, 2013, at 5:19 PM, Steve Lianoglou wrote: > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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