Programmatic access to the Genome Browser

• Get the sequence of a genome at a particular place
  • Download the tool twoBitToFa from http://hgdownload.cse.ucsc.edu/admin/exe/
  • twoBitToFa http://hgdownload.cse.ucsc.edu/gbdb/hg19/hg19.2bit test.fa -seq=chr21 -start=1 -end=10000
  • for best performance, download the 2bit file for your genome from http://hgdownload.cse.ucsc.edu/gbdb/<databaseId> to local disk.

• Get the "wiggle" (x-y-plot) graph data
  • Download bigWigToWig from http://hgdownload.cse.ucsc.edu/admin/exe/
  • bigWigToWig http://hgdownload.cse.ucsc.edu/gbdb/hg19/bbi/wgEncodeBroadHistoneK562Cbx2Sig.bigWig -chrom=chr21 -start=0 -end=10000000 stdout

• Download data from a database table

• • use Tools - Table Browser - "Describe schema" to browse the database schema. All fields have a human readable description and the links to other tables are shown.
  • mysql --no-defaults -h genome-mysql.cse.ucsc.edu -u genome -A -e 'select * from pubsBingBlat' -NB > out.txt

• Get a copy of the current Genome Browser image from a script
  • use "curl http://genome.ucsc.edu/cgi-bin/hgRenderTracks > test.png". hgRenderTracks understands the same parameters and options as the main hgTracks CGI, e.g. <trackName>=pack.
  • to show only a single track with hgRenderTracks, make sure that the first track parameter is hideTracks=1
  • for example, to download the image for a chromosomal location with only the RefSeq transcripts and publications track to "pack" mode, use this command:

  curl 'http://genome.ucsc.edu/cgi-bin/hgRenderTracks?position=chr17:41570860-41650551&hideTracks=1&refGene=pack&pubs=pack' > temp.png 

• Upload a custom track and link to the genome browser with the track loaded

• • create a file temp.bed with contents like these:

 track name="TestTrack" description="TestTrack with links on features" url="http://www.google.com/$$"
 chr1 1 1000 testIdForUrl

• • upload your file with a command like this, it will print a string to stdout which we are calling $HGSID in the following

 curl -s -F db=hg19 -F 'hgct_customText=chr1 1 1000' http://genome.ucsc.edu/cgi-bin/hgCustom  | grep -o 'hgsid=[0-9]*_[a-zA-Z0-9]*' | uniq | sed -e 's/hgsid=//'

• • you can link to this track with http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=$HGSID&position=chr1:1-1000