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 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:
- mutation types. e.g. CG -> AT, CG -> TA etc. polarized with the relative genomes
- Polymorphism along chromosomes (or scaffold)
- Polymorphism by type; intergenic, CDs etc.; and polymorphism by metabolic network
- LD and recombination
- drastic mutations. e.g. stop codons etc. in gene family, Gene Ontology
- Population structure using STRUCTURE
- Fst among groups
- association studies