How can I use Annotatr on CDS?
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xie186 • 0
@xie186-11029
Last seen 21 days 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 • 583 views
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rcavalca ▴ 140
@rcavalca-7718
Last seen 2.7 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.

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

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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. 

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