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

How to Create a Filter Program in the UCSC Genome Browser at ENCODE

• 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
2. 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):
3. 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.