Thank you so much Steve.


On 23 March 2011 17:58, Steve Lianoglou <mailinglist.honeypot@gmail.com>wrote:

> Hi,
>
> On Wed, Mar 23, 2011 at 12:14 PM, Vincenzo Capece <vivo0304@gmail.com>
> wrote:
> > Dear all,
> > i am a beginner.
> > This is my first post and i hope it is clear.
> > I'm developing a pipeline to analyze DNA reads from NGS machines.
> > Now, after the alignemnt and the study of the SAM file,  i have a
> file.vcf
> > and a file.snp about the structural variations of the DNA code.
> > Now i want to manage those files (SAM/BAM, snp and vcf) with Bioconductor
> > packages for a statistical  analysis of my variations.
> > It's possible with R?
> > If yes, what do you suggest?
>
> Use Rsamtools to interface with your BAM files.
>
> I have no idea what type of data you have in your *.vcf and *.snp
> files, so I can't comment on that.
>
> I think the best advice I can give you is that if you are trying to
> analyze NGS data, you should get to know the IRanges, GenomicRanges,
> GenomicFeatures, Biostrings, BSgenome.*, and Rsamtools  packages very
> intimately.
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>



-- 
Regards,
            Capece Vincenzo

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