cpgIslandExt

[Longjin Zeng]

Dear Members,

Can you tell me the source of the data annotation, because CpG sites should be obtained from sequencing. At present, I only know this calculation method (http://genomewiki.ucsc.edu/index.php/CpG_Islands).

Thank you very much for your attention and consideration.

Sincerely yours,

Longjin Zeng

[Longjin Zeng]

[Gerardo Perez]

Hello, Longjin.

Thank you for your interest in the UCSC Genome Browser and for your question about the cpgIslandExt track.

The CpG Islands in this track are not derived from sequencing. They were predicted by searching the sequence one base at a time, scoring each dinucleotide (+17 for CG and -1 for others). Maximally scoring segments were then identified that met 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

You can find more details on the track description page: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&position=default&g=cpgIslandExt#TRACK_HTML

This track was generated using a modification of a program developed by G. Miklem and L. Hillier. The source code is available at: https://github.com/ucscGenomeBrowser/kent/tree/master/src/utils/cpgIslandExt

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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