On Mon, Dec 6, 2010 at 6:28 AM, Mao Jianfeng <jianfeng.mao@gmail.com> wrote:

> Dear bioconductor listers,
>
> I just move from classical population genetics to genomics/population
> genomics. I need to set up my genomic handling platform and ability. I
> have used R for statistics for 3 years, so bioconductor is preferable
> to me.
>
> In my current study, we sequenced genomes of tens of accessions of a
> plant, by Illumina next generation sequencer. And, now the reads have
> been aligned with the reference genome.
>
> I have not any experiences of genomic analysis. On the beginning, I
> checked all the available packages for sequence analyses of the
> bioconductor, and read their manual. And also, I surveyed the courses
> in bioconductor websites. But, I still can not make a full and
> effective workflow for me to do population genomic analysis, though I
> have witnessed much excellent genomic implements of bioconductor.
>
> I think an effective workflow to do population genomic analysis by
> using R platform is very valuable for all of us who are/will be
> genomicers. Thank you for your helps in advance.
>
> I need hints, tips, suggestions, and advice on making an explicit and
> effective workflow for me to do the following analysis by using
> bioconductor or maybe not:
>
> 1. mutation types. e.g. CG -> AT, CG -> TA etc. polarized with the
> relative genomes
> 2. Polymorphism along chromosomes (or scaffold)
> 3. Polymorphism by type; intergenic, CDs etc.; and polymorphism by
> metabolic network
> 4. LD and recombination
> 5. drastic mutations. e.g. stop codons etc. in gene family, Gene Ontology
> 6. Population structure using STRUCTURE
> 7. Fst among groups
> 8. association studies
>
>
Thanks for listing these requirements. I think there's a dearth of
functionality for this in Bioc right now, but I would be happy to be
corrected. Martin has recently added BCF import to Rsamtools, so at least we
can get the variants into R.


> --
> Jian-Feng, Mao
>
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