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 [[alternative HTML version deleted]]

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 [[alternative HTML version deleted]]