[BioC] How to plot NGS data?

[Martin Morgan]

On 02/15/2012 06:14 AM, Bernd Jagla wrote:
>
> Hi,
>
> I have "a few" reference genomes from NGS resequencing experiments and
> annotation in GFF format that I would like to use in some of the
> plotting functions that are available (i.e. geneplotter, ChromHeatMap).
> Actually, I would to integrate these with expression results from
> correlated NGS RNA-seq experiments.

Hi Bernd -- maybe good places to start are the ggbio vignette, available 
as a PDF on the page at

http://bioconductor.org/packages/release/bioc/html/ggbio.html

and the Gvis vignette (if you're willing to use the 'devel' version of R 
and Bioconductor)

   http://bioconductor.org/packages/2.10/bioc/html/Gviz.html

Both might give you an idea of the possibilities. library(ShortRead); 
example(Snapshot) might also be a lighter-weight starting point.

If you're able to say more precisely what you'd like, and where you're 
starting from (presumably BAM files, but maybe hints about organism, 
purpose of experiment, what you're hoping to get out of the 
visualization...), perhaps someone on the list will be able to provide 
some more explicit suggestions.

Hope that provides some help. Martin

>
> My overall approach currently includes using BSGenome,
> GenenicFeature/FeatureDb, expressionSet and geneplotter/ChromHeatMap.
>
> I haven't figured out how to fill an expressionSet class with my counts
> and how to define regions / genes. Also, is this the class to use? There
> seem to be too many possible routes to go and I am feeling quite lost...
>
> I am now in the process of creating a BSGenome object using
> BSGenomeForge, which seems to be working.
>
> As all this seems to be quite complicated and I haven't found a complete
> guide on how to visualize NGS results I would like to verify this
> approach by someone and maybe get some pointers to help me on how to do
> visualization with RNA-seq experiments...
>
> Thanks a lot for your kind help and consideration.
>
> Bernd,
>
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