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Old 01-10-2013, 10:30 PM   #2
cwhelan
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Location: Cambridge, MA

Join Date: Nov 2010
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This is normal although it should only happen in a few regions. This paper suggests that it is due to misassembled regions of the reference where there should be many copies of a repeat but there's only one in the assembly:

http://bioinformatics.oxfordjournals...rmatics.btr354

You could check the BED files linked to from that paper to see if they match up with your high peaks.
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