Question: How can I use Annotatr on CDS?
0
gravatar for xie186
21 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.

exon cds utr annotatr • 361 views
ADD COMMENTlink modified 21 months ago by rcavalca130 • written 21 months ago by xie1860
Answer: How can I use Annotatr on CDS?
1
gravatar for rcavalca
21 months ago by
rcavalca130
United States
rcavalca130 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 21 months ago by rcavalca130

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

ADD REPLYlink written 21 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 21 months ago by xie1860
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