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Old 08-30-2013, 01:20 PM   #4
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
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In addition to what rboettcher said, have a look at where some of these intergenic regions are in relation to known/predicted repeats motifs, such as IAPs or LINES (there are repeatmasker tracks available). I suspect that a lot of these a just these repeat elements. Depending on the nature of your KO lines, these may or may not be functionally meaningful (there's a lot of transcriptional noise that never amounts to much of anything).
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