Question: How can I use Annotatr on CDS?
gravatar for xie186
11 days ago by
xie1860 wrote:

I'm using Annotatr on mm10.

#annots =c('mm10_cpg_islands', 'mm10_cpg_shores', 'mm10_cpg_shelves', 'mm10_cpg_inter')
annots = c('mm10_genes_promoters',
# Build the annotations (a single GRanges object)
annotations = build_annotations(genome = 'mm10', annotations = annots)

UTRs are already included in exons. Is there a way that I can use CDS instead of exons here? Thanks.

ADD COMMENTlink modified 11 days ago by rcavalca90 • written 11 days ago by xie1860
gravatar for rcavalca
11 days ago by
United States
rcavalca90 wrote:

Hi, thanks for using annotatr.

The CDS can be used with mm10_genes_cds. For a visual idea of where that falls:

Hope that answers your question.

ADD COMMENTlink written 11 days ago by rcavalca90

 I was using 'CDS' instead of 'cds', so it didn't work out. Thanks for developing such a nice package.

ADD REPLYlink written 11 days ago by xie1860

Hi @rcavalca, I'm wondering that whether the parameter "fill_order" is just for the order of the legend? Or it will also be applied to priority information. For example, if there is a region that overlap with both CDS and UTR. The fill order is c("UTR", "CDS"). Will both of them be considered or just "UTR" be considered? Thanks. 

ADD REPLYlink written 9 days ago by xie1860
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