Haynes Lab:Notebook/Synthetic Biology and Bioinformatics for Predictable Control of Therapeutic Genes/2012/01/25

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  • Received a response from the UCSC Genome Browser at ENCODE. All future Genome Browsing will following the filter protocol below.
  1. Create a custom track containing transcription start positions + and - 500bp, and intersect it with the following tables in the Table Browser:

wgEncodeUwHistoneHepg2H3k27me3StdPkRep1 wgEncodeUwHistoneHepg2H3k27me3StdPkRep2 wgEncodeUwHistoneBjH3k27me3StdPkRep1 wgEncodeUwHistoneBjH3k27me3StdPkRep2

  1. To find the actual transcription start positions, you will need to query the knownCanonical table in the Table Browser (to get only one isoform). You will also need to filter by strand on the knownGene table by clicking on the 'create' button next to 'filter:', and setting 'strand does match +' (for the positive strand). You can retrieve the chrom and chromStart by choosing 'selected fields from primary and related tables' as the output format, and selecting those fields on the following page. Then you will need to add 1 to chromStart to get the 3rd field of the BED file. You can do this using excel or if you are familiar with bash (or tc shell) you could use that too. You should then have a BED file looking like this example (for the + strand):

track name="+ strand canonical starts" chr1 11873 11874 chr1 69090 69091 chr1 321083 321084 chr1 321145 321146 chr1 322036 322037 chr1 367658 367659 chr1 420205 420206 chr1 566461 566462 chr1 568148 568149

  1. Then, you could use the Table Browser (or Excel or a script) to retrieve a BED file with +/- 500bp. For the negative strand genes, you would need to query the Table Browser for chromEnd.


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