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Old 05-24-2013, 07:34 AM   #8
timforshew
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Location: Cambridge, UK

Join Date: Jun 2011
Posts: 6
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Some regions are essentially impossible to look at specifically if you have short amplicons as there is so much similarity between PTEN and PTENP1. If you blat PTENP1 against PTEN you can spot the few locations they differ at then place the 3' end of your primers on them (although there still maybe be problems). Out of interest are you limited because of the MiSeq read length or because your DNA is degraded? We work with degraded DNA but if yours isnt you could use larger amplicons to "anchor" in specific regions and just tile more. Best wishes, Tim
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