[Genome] apparent contradiction in genome graphs

[Ann Zweig]

Hello Horia,

	The way the Genome Graphs tool splits significant values into regions is not 
always intuitive.  There are several dependencies.  There is a discussion of 
significant regions and thresholds in the User's Guide here:
http://genome.ucsc.edu/goldenPath/help/hgGenomeHelp.html#SigThreshold

	If this doesn't shed any light on your question, please send the screen shots, 
data file, and Genome Graph settings directly to me and I'll be happy to take a 
look at your specific situation.

	By the way, our mail program does not accept attachments; screen shots and the 
like are stripped before the message is delivered.


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu




Stanescu, Horia (NIH/NHGRI) [F] wrote:
> Hello,
> 
> Plotting my dataset in genome graphs I obtained screenshot 1.
> 
> Upon its inspection I was expecting to obtain only one region after
> setting the significance threshold at 0.6 and clicking 'browse regions'.
> 
> To my surprise I got 4 non contiguous regions (attached screenshot 2)!
> 
> Can you please tell me what the explanation might be?
> 
> Thank you for your help,
> 
> Horia Stanescu
> 
> 
> 
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