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Old 06-02-2011, 02:53 AM   #2
Location: Paris

Join Date: Jun 2011
Posts: 15

I have just found a topic which gave me a possible answer...
Topic of NGSfan untitled Agilent SureSelect - coverage of high GC regions.

Apparently, as shown in the paper of Tewhey et al (2009 Genome Biol), the regions of high GC content were difficult to capture.
So, I checked with my sample calculating the GC % between regions with a low and high density of reads.
Effectively, I obtained around 65-70% of GC in the regions with low density of reads and 45-50% of GC in the regions with normal or high density of reads. So, there is a real difference.
According to this result, it seems that the problem would come from a bad hybridization between the baits and my DNA because of too high GC %.

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