On Wed, Nov 19, 2008 at 11:13 AM, Paul Hammer <paul.hammer@p-t-p.de> wrote:

> Dear all,
>
> I have solexa sequence data (rat) and I would like to plot the
> expression values directly in a genome browser, preferably Ensembl
> Genome Browser. Now  I am looking for packages that deal with this
> stuff. Until now I've found the packages "rtracklayer", "xmapbridge" and
> "GenomeGraphs". These packages are a good start but I am not sure if
> they are sufficient.
>
> I like the "xmapbridge" package but I am not sure if you are able to
> save high quality pictures for publications. I guess the only way to do
> this is via the sreenshot function of the OS. Is that right and is that
> acceptable?
>
> Maybe somebody have experience with plotting 2nd generation sequencing
> data. One feature should be also to generate plots for showing the
> splicing variants / exon junction reads in a nice way. One good way
> would be plotting the read counts directly into the genome browser.
>
> But anyway some experiences or preferences would be great.
>

You might also want to look at IGV.  It is not an R solution, but....

http://www.broad.mit.edu/igv/

Sean

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