Question

Extracting gene structures from a GFF3 file for use with annotateWithGeneParts()

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alan.g.hudson • 0

@alanghudson-16729

Last seen 19 months ago

United States

Hi,

I want to use genomation to annotate previously identified differentially methylated genomic regions and quantify the overall degree of overlap with different gene structures (promoters, TSSs, exons, introns, intergenic).

The annotation file for my specific reference genome is in GFF3 format. Whilst it seems relatively straight forward to use BED 12 format to extract the relevant genomic coordinates using readTranscriptFeatures() - I can't figure out how to do the same for a GFF3 format annotation file.

I have looked at GenomicFeatures and there it seems possible to extract some of the features listed above (promoters, exons, introns) but this would result in a mix of several GRanges and GRanges list objects and again I have no idea how to combine these objects into the single object of the right format to plug into annotateWithGeneParts()

Has any one successfully dealt with a similar situation and can give some advice? Alternatively, if anyone can suggest another annotation strategy that would also be gratefully received?

Cheers,

Alan

genomicfeatures genomation genomicranges methylation annotation • 2.4k views

ADD COMMENT • link updated 6.3 years ago by altuna akalin ▴ 20 • written 6.3 years ago by alan.g.hudson • 0

score 1 · Answer 1 · 2018-07-31

I already answered this exact question here: https://groups.google.com/forum/#!topic/genomation/5EFpaBBEWLQ you can do that if you can create a GRanges list that has the same structure with readTranscriptFeatures() output. It returns a GRangesList most likely or simple list with GRanges (I think it has TSS, exon, intron and promoter GRanges objects). You just have to replicate the order and the structure of that output then downstream stuff from genomation should work. On Tue, Jul 31, 2018 at 10:32 PM alan.g.hudson [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User alan.g.hudson <https: support.bioconductor.org="" u="" 16729=""/> wrote Question: > Extracting gene structures from a GFF3 file for use with > annotateWithGeneParts() <https: support.bioconductor.org="" p="" 111565=""/>: > > Hi, > > I want to use genomation to annotate previously identified differentially > methylated genomic regions and quantify the overall degree of overlap with > different gene structures (promoters, TSSs, exons, introns, intergenic). > > > > The annotation file for my specific reference genome is in GFF3 format. > Whilst it seems relatively straight forward to use BED 12 format to extract > the relevant genomic coordinates using readTranscriptFeatures() - I can't > figure out how to do the same for a GFF3 format annotation file. > > > > I have looked at GenomicFeatures and there it seems possible to extract > some of the features listed above (promoters, exons, introns) but this > would result in a mix of several GRanges and GRanges list objects and again > I have no idea how to combine these objects into the single object of the > right format to plug into annotateWithGeneParts() > > > > Has any one successfully dealt with a similar situation and can give some > advice? Alternatively, if anyone can suggest another annotation strategy > that would also be gratefully received? > > > > Cheers, > > > > Alan > ------------------------------ > > Post tags: genomicfeatures, genomation, genomicranges, methylation, > annotation > > You may reply via email or visit > Extracting gene structures from a GFF3 file for use with annotateWithGeneParts() >