Dear Colleague,
For the hg18 CpG island track which can be downloaded from
ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/cpgIslandExt.txt.gz
• 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
Besides the above three criteria, does your method exclude repeat sequences
(Alu)
before calculating the CpG island?
Some one else asked a similar question below.
However, the answer is not clear to me
I don't understand
"We run cpglh on sequence that has been hardmasked (Ns) where
RepeatMasker or TRF (period <= 12) has found repetitive sequence"?
Did you run cpglh on repeat sequences only?
Thanks,
Bests,
Hao
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[Genome] CpG island calculation method
Angie Hinrichs angie at soe.ucsc.edu
Fri Mar 5 13:33:22 PST 2004
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Dear Meg,
We use the cpglh program from Washington University (St. Louis) Genome
Sequencing Center. The original author was Gos Miklem from the Sanger
Center. The version we use has been modified by LaDeana Hillier at
WUGSC. If you are an academic or non-profit user, we could send you a
copy of the source.
We run cpglh on sequence that has been hardmasked (Ns) where
RepeatMasker or TRF (period <= 12) has found repetitive sequence.
Angie
On Fri, 5 Mar 2004, Megumi Sakai wrote:
> Dear Sir or Madam,
>
> I have a question about CpG island track in UCSC genome brwoser.
> Does this track include repeat sequences (Alu)?
> Does your method exclude repeat sequences before the CpG calculation?
>
> Meg
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