Question: How are rat genome's CpG islands calculated?
0
gravatar for biocyberman
11 months ago by
biocyberman640
Denmark
biocyberman640 wrote:

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

cpg islands ucsc • 354 views
ADD COMMENTlink modified 11 months ago by jotan1.1k • written 11 months ago by biocyberman640
2
gravatar for sysbiocoder
11 months ago by
sysbiocoder170
sysbiocoder170 wrote:

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"

ADD COMMENTlink written 11 months ago by sysbiocoder170

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

ADD REPLYlink written 11 months ago by biocyberman640
2
gravatar for jotan
11 months ago by
jotan1.1k
Australia
jotan1.1k wrote:

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

ADD COMMENTlink written 11 months ago by jotan1.1k
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