On Thu, Jul 30, 2009 at 12:52 AM, Michael Dondrup <
Michael.Dondrup@bccs.uib.no> wrote:

> Dear BioC list,
>
> I'm trying to use the package GenomeGraphs to visualise custom genome data
> (genome not in public databases). In the corresponding publication to
> genomegraphs (Durinck et al. BMC Bioinformatics, 2009 ) I found the partial
> clue: "... genomic annotation encoded in GFF files can be easily used to
> create a custom AnnotationTrack object for visualization... region start,
> and end positions need to be given, as well as how these regions are to be
> grouped."
> This leaves me with two questions:
> - I have no idea how to parse a GFF file, is there a GFF parser in
> Bioconductor?
>

Yes, rtracklayer has a parser. Please see the vignette.


>
> - If I have such GFF file for a genome, how can I create such an
> AnnotationTrack with all CDS?
>
> Hope somebody can help me with one of this.
>
> Best
> Michael
>
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