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 [[alternative HTML version deleted]]