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.

Thanks in advance,
Paul

-- 
Paul Hammer, M.Sc.
Philips Ph.D. student

University of Applied Sciences Wildau
Department Bioinformatics
Bahnhofstrasse 1
15745 Wildau
Germany
paul.hammer@tfh-wildau.de

house 13, room 120
phone +49 (0) 3375 508 945
fax +49 (0) 3375 508 946 	
	Neurochemistry Group and Mouse Lab
Dept. Ropers for Human Genetics
Max-Planck Institute for Molecular Genetics
Ihnestrasse 73
15475 Berlin
Germany

hammer_p@molgen.mpg.de
phone +49 30 8413 1664


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