Question

How can I use Annotatr on CDS?

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xie186 • 0

@xie186-11029

Last seen 3.2 years ago

USA

I'm using Annotatr on mm10.

library(annotatr)
#annots =c('mm10_cpg_islands', 'mm10_cpg_shores', 'mm10_cpg_shelves', 'mm10_cpg_inter')
annots = c('mm10_genes_promoters',
    'mm10_genes_5UTRs',
    'mm10_genes_3UTRs',
    'mm10_genes_exons',
    'mm10_genes_introns',
     "mm10_genes_1to5kb",
    'mm10_genes_intergenic')
# 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.

Annotatr CDS Exon UTR • 1.6k views

ADD COMMENT • link updated 6.8 years ago by rcavalca ▴ 140 • written 6.8 years ago by xie186 • 0

score 1 · Answer 1 · 2018-02-13

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rcavalca ▴ 140

@rcavalca-7718

Last seen 5.9 years ago

United States

Hi, thanks for using annotatr.

The CDS can be used with mm10_genes_cds. For a visual idea of where that falls: http://bioconductor.org/packages/release/bioc/vignettes/annotatr/inst/doc/annotatr-vignette.html#genic-annotations

Hope that answers your question.

ADD COMMENT • link 6.8 years ago rcavalca ▴ 140

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

ADD REPLY • link 6.8 years ago xie186 • 0

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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 REPLY • link 6.8 years ago xie186 • 0