[BioC] How to plot NGS data?

[Bernd Jagla]

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.

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,