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
•
written
by
jonessara770
1 answer
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.
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