Hi David, Sorry for the delayed response. If you click on an item in the CpG Islands track or click on the track name on the main Genome Browser display page (http://genome.ucsc.edu/cgi-bin/hgTracks), you will see a description of the criteria used to create the items in the track. For hg19, the description includes:
--- Methods CpG islands were predicted by searching the sequence one base at a time, scoring each dinucleotide (+17 for CG and -1 for others) and identifying maximally scoring segments. Each segment was then evaluated for the following criteria: GC content of 50% or greater length greater than 200 bp ratio greater than 0.6 of observed number of CG dinucleotides to the expected number on the basis of the number of Gs and Cs in the segment --- Note that the CpG island detector program is run on repeat-masked sequence. See this previously-answered question for more details: https://lists.soe.ucsc.edu/pipermail/genome-mirror/2010-September/002087.html If you still think there is an issue with the track, please send us an example region, and be sure to include the name of the assembly you are looking at (hg18, hg19, mm9, etc.). Please reply to [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/7/11 5:56 PM, David Shames wrote: > Has anyone noticed any recent issues with the CpG island track? In the > past couple of days I've noticed that track has missed what should have > been called CpG islands in at least 2 genes. > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
