PGS Documentation

Page tree

Versions Compared


  • This line was added.
  • This line was removed.
  • Formatting was changed.


  • Go to UCSC Genome Browser
  • Select Table Browser under Tools in the main command bar of the webpage (Figure 1)

Numbered figure captions
SubtitleTextNavigating to the Table Browser at the UCSC Genome Browser website
AnchorNameUCSC Genome Browser

Image Modified

  • Configure the Table Browser page as shown (Figure 2) 

Numbered figure captions
SubtitleTextConfiguring the Table Browser to output CpG Islands BED file
AnchorNameConfiguring Table Browser
Image Modified
  • Set assembly to Feb. 2009 (GRCh37/hg19)
  • Set group to Regulation
  • Set track to CpG Islands
  • Set table to cpgIslandExt
  • Set output format to BED 
  • Set output file to cpg.bed
  • Select get output 


For this region list, you can also calculate the average beta values for the probes in each island per sample and detect differential methylated CpG islands regions. Detailed information on how to get average beta value for each CpG can be found in the Determining the average values for a region list section of Starting with a list of genomic regions.   

Additional assistance


Rate Macro