[BioC] about the annotate the new genome for geneplotter/genegraph

Michael Dondrup Michael.Dondrup at bccs.uib.no
Fri Jul 31 11:06:39 CEST 2009

Dear Zhuo-Cheng,

I am currently having a similar problem using the GenomeGraphs  
package. It seems that as long as you are
doing mainstream, like human, mouse, things are fine, very easy to  
work with these packages, but as soon as you try
something that is a little more uncommon, you are immediately out of  
luck, because you either need a genome in a certain database
or a custom made dataset like the hgu-something. Also, there seems to  
be almost no documentation for this task. So I think there is  
definitely room for improvement here.

Thanks to kind help from the list I figured out how to read in a GFF  
file using rtracklayer. Now I am trying to make a plot of the genome  
imported from a file using genomegraphs. If I succeed, I can share the  
results, although I am no sure if that visualization is what you need.


Am 31.07.2009 um 02:28 schrieb zhuocheng Hou:

> Hi All,
> We want to use geneplotter/geneGraph to map the gene expression on  
> each
> chromosome for opossum/platypus/or any other genome which not  
> supported by
> bioconductor genome datasets. We had mapping position for each gene  
> on each
> chromosome. How do we write the data for using geneplotter/geneGraph?
> For example, buildChromLocation doesn't support these genomes, how  
> do we
> build the similar annotation data as BioC did for human/mouse?
> Thanks,
> Zhuo-Cheng
> 	[[alternative HTML version deleted]]
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