How are rat genome's CpG islands calculated?
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4.3 years ago
biocyberman ▴ 810

I am looking at this file, and could not find description about its format and how it is generated from rat genome. Can someone give some info about it? http://hgdownload.cse.ucsc.edu/goldenpath/rn6/database/cpgIslandExt.txt.gz

ucsc cpg islands • 1.1k views
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4.3 years ago
sysbiocoder ▴ 180

Here are column labels
"Chromosome or FPC contig" chromStart; "Start position in chromosome" chromEnd; "End position in chromosome" name; "CpG Island" length; "Island Length" cpgNum; "Number of CpGs in island" gcNum; "Number of C and G in island" perCpg; "Percentage of island that is CpG" perGc; "Percentage of island that is C or G" obsExp; "Ratio of observed(cpgNum) to expected(numC*numG/length) CpG in island"

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@sybiocoder Can you give a link to document that describes this?

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4.3 years ago
jotan ★ 1.2k

Click on the CpGi track control on the browser window

Basically arbitrary conditions:

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

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