Reading GFF files into R and GenomeGraphs
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@michael-dondrup-3591
Last seen 7.9 years ago
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? - 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
Annotation GenomeGraphs Annotation GenomeGraphs • 1.4k views
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@michael-lawrence-2759
Last seen 7.9 years ago
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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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