Hello, I recently downloaded the cpgIslandExt table for Human genome GRCh37. Whilst using this file in an analysis, I stumbled upon a problem, the root of which seemed to come back to the cpgIsland file. It seems that, for some islands, the metadata is incorrect. For example:
http://genome.ucsc.edu/cgi-bin/hgc?hgsid=171991065&o=33697914&t=33698193&g=c pgIslandExt&i=CpG%3A+22 This cpg island has a CpG count of 22. However on inspection of the sequence, the actual count can be seen to be 29. Hence the percentage CpG and ratio of observed/expected will also be incorrect. Am I missing something obvious? And if not, have you any idea as to how many islands have similar errors? Hope you can help! Thanks Gareth Wilson _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
