How to receive annotation files from dump of the UCSC genome annotation database for given genome.

[alexg9010]

If you do not want to use the table browser to retrieve the annotation files in bed format you could also do it programmatically.

Before running this code you may want to verify that the required files actually exists in the UCSC annotation dump for your genome, by navigating to the http://hgdownload.cse.ucsc.edu/goldenpath/{{GENOME}}/database/ URL (replace {{GENOME}} with your genome of interest).

This code exemplifies how to fetch and convert bed files for hg19 assembly. This requires the bedops tool.

fetch-cpg:

wget -qO- http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/cpgIslandExt.txt.gz \
  | gunzip -c \
  | awk 'BEGIN{ OFS="\t"; }{ print $$2, $$3, $$4, $$5$$6, substr($$0, index($$0, $$7)); }' \
  | sort-bed - | gzip > cpgIslandExt.hg19.bed.gz

fetch-ref:

wget -qO- http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/refGene.txt.gz \
  | gunzip -c \
  | awk 'BEGIN{ OFS="\t"; }{ print $$3, $$5, $$6, $$2, $$12, $$4, $$7, $$8; }' \
  | sort-bed - | gzip > refGene.hg19.bed.gz