On Thu, May 12, 2011 at 4:26 AM, Vincenzo Capece <vivo0304@gmail.com> wrote:

> Dear all,
> i am a beginner, i hope you can help me.
> I aligned my reads file and now i have a BAM file.
> Now i want to divide the genome in genes.
> Is possible to do it?
> If yes, how?
> >From bam file is possible to extract a SNP for a particular gene?
> Example:
> I want something like:
> gene x:
> snp in base: 43, 120 45
>
> gene y:
> snp in base: 56, 78, 540
> and so on..
>
>
Hi, Vincenzo.  From your questions, I think you might be well-served by
finding a bioinformatics collaborator to work with you.  That said, look
into using samtools mpileup or GATK for SNP calling.  After the actual
variant calls are made, then determining which gene, etc., can be done using
bioconductor, but there are a number of non-bioconductor tools specifically
designed for that including snpEff, annovar, xvar, and ensembl variant
effect predictor (and several others).

Sean


> >From these results, is possible to have a plot?
>
> I hope that these questions are right and clear.
> Thanks for the attention to all.
>
> Regards,
>            Vincenzo
>
> --
> Regards,
>            Capece Vincenzo
>
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>
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