annotate bed file with CCDS

Question

[jonessara770]

Hello,

I have a bed file (chr start end) and I want to know how to annotate them with CCDS and get the following format:

Example chr start end 10 100177320 100177483 HPS1|NM_000195_cds_0 10 100177931 100178014 HPS1|NM_000195_cds_0

Thanks Sara

Answer 1

[Alex Reynolds]

You could download CCDS as BED from the UCSC Genome Browser, and then perform a BEDOPS bedmap operation over your regions of interest (e.g., roi.bed) and the CCDS dataset (e.g., ccds.bed):

$ bedmap --echo --echo-map-id-uniq roi.bed ccds.bed > answer.bed

The file answer.bed will have each region of interest (ROI). The final column of each ROI will be a semi-colon-delimited string of CCDS ID values, for CCDS annotations that overlap each ROI.

Other --echo-map-* options are available, if you need more than the ID value. See the documentation for more information.