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rcavalcante / annotatr

Package Homepage: http://bioconductor.org/packages/devel/bioc/html/annotatr.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=annotatr.
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hg38 CGI annotation #47

Closed magdadrozdz closed 2 years ago

magdadrozdz commented 2 years ago

Hi, I was wondering where the data for hg38 CpG islands come from. The intro online mentions it is obtained from the AnnotationHub package, but when I looked at the available annotations there it only includes hg18, hg19 and no hg38. How did you obtain it? Did you liftover from hg19?

rcavalcante commented 2 years ago

Hi there,

It looks like annotatr is using UCSC, and not the AnnotationHub. This link in particular: http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/cpgIslandExt.txt.gz

Sorry, I should clarify the documentation, my mistake.

Thanks, Raymond