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Question: How can I use Annotatr on CDS?
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gravatar for xie186
7 months ago by
xie1860
USA
xie1860 wrote:

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.

ADD COMMENTlink modified 7 months ago by rcavalca120 • written 7 months ago by xie1860
1
gravatar for rcavalca
7 months ago by
rcavalca120
United States
rcavalca120 wrote:

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 COMMENTlink written 7 months ago by rcavalca120

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

ADD REPLYlink written 7 months 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 7 months ago by xie1860
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