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Old 07-28-2016, 11:59 PM   #2
tristan dubos
Location: France

Join Date: Dec 2015
Posts: 39

I was with the same problematic when I studies repeats region to determine number copy. I saw in BWA(mem) no mapping to the extremity of my reference (500 bases). To solve the problem by put 2 times my references aside. I tried before this to put N to the extremity of the references and low stringency alignment parameters but i was i low complexity sequences the i had everything mapping on the position that is why i used the first solution.
I hope it could help

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