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CpG island track [message #7472] Wed, 07 December 2011 16:56 Go to next message
David Shames  is currently offline David Shames
Messages: 1
Registered: December 2011
Junior Member
Has anyone noticed any recent issues with the CpG island track? In the
past couple of days I've noticed that track has missed what should have
been called CpG islands in at least 2 genes.

--
David S. Shames, PhD.
Genentech Inc.,
Development Oncology Diagnostics
Office: 650-225-7559
Shames.David@gene.com
_______________________________________________
Genome maillist - Genome@soe.ucsc.edu
https://lists.soe.ucsc.edu/mailman/listinfo/genome
Re: CpG island track [message #7594 is a reply to message #7472] Mon, 19 December 2011 12:25 Go to previous message
Brooke Rhead  is currently offline Brooke Rhead
Messages: 955
Registered: June 2010
Senior Member
Hi David,

Sorry for the delayed response. If you click on an item in the CpG
Islands track or click on the track name on the main Genome Browser
display page (http://genome.ucsc.edu/cgi-bin/hgTracks), you will see a
description of the criteria used to create the items in the track. For
hg19, the description includes:

---
Methods

CpG islands were predicted by searching the sequence one base at a time,
scoring each dinucleotide (+17 for CG and -1 for others) and identifying
maximally scoring segments. Each segment was then evaluated for 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 on the basis of the number of Gs and Cs in the segment
---

Note that the CpG island detector program is run on repeat-masked
sequence. See this previously-answered question for more details:

https://lists.soe.ucsc.edu/pipermail/genome-mirror/2010-Sept ember/002087.html

If you still think there is an issue with the track, please send us an
example region, and be sure to include the name of the assembly you are
looking at (hg18, hg19, mm9, etc.). Please reply to genome@soe.ucsc.edu.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



On 12/7/11 5:56 PM, David Shames wrote:
> Has anyone noticed any recent issues with the CpG island track? In the
> past couple of days I've noticed that track has missed what should have
> been called CpG islands in at least 2 genes.
>
_______________________________________________
Genome maillist - Genome@soe.ucsc.edu
https://lists.soe.ucsc.edu/mailman/listinfo/genome
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