Hi, I am trying through the packages that's been suggested. My sincere thankfulness for your guidance. Thanks & regards, Jayakumar S On Thu, Sep 26, 2013 at 12:29 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 9/25/2013 3:45 PM, jayakumar sivalingam wrote: > >> Hello, >> Please let me know about the bioconductor packages to be used for the >> following things: >> >> >> 1. Quality check of the whole genome raw data >> 2. Alignment >> 3. SNP identification >> > > In addition there is VariantTools (Linux only) > > http://bioconductor.org/**packages/release/bioc/html/**VariantTool s.html<http: bioconductor.org="" packages="" release="" bioc="" html="" varianttools="" .html=""> > > 4. Annotation >> > > http://bioconductor.org/help/**workflows/variants/<http: biocondu="" ctor.org="" help="" workflows="" variants=""/> > > also of interest > > http://bioconductor.org/**packages/release/bioc/html/** > AnnotationHub.html<http: bioconductor.org="" packages="" release="" bioc="" htm="" l="" annotationhub.html=""> > http://bioconductor.org/help/**community/<http: bioconductor.org="" help="" community=""/> > http://bioconductor.org/help/**course- materials/2013/**SeattleMay2013/<http: bioconductor.org="" help="" course-="" materials="" 2013="" seattlemay2013=""/> > > > >> Also, please let me know how I can be able to practice the above things >> with the example data and the system requirements for the same. >> > > Many packages come with sample data sets; many vignettes and work flows > are fully executable, look for the 'R script' on package help pages and > package landing pages. > > Packages usually operate 'across platforms' and many do not have > third-party software requirements, although there are exceptions; actual > system resources (e.g., memory) used vary by package and problem. > > Martin > > > >> Thanks & regards, >> Jai >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> >> > > -- > Dr. Martin Morgan, PhD > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > [[alternative HTML version deleted]]