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Old 11-07-2012, 05:19 AM   #1
Location: Cambridge

Join Date: Oct 2011
Posts: 12
Default huge difference in alignment by strand?


I found there were huge difference in alignment by strand in my paired-end DNA sequence data. The samples were sequenced using Miseq. Each read is about 220bp long and my target gene is about 240bp long. So there are overlaps between a pair.

For example, given 17500 reads, for forward reads 808 are mapped while in the reverse case 16447 are mapped. I used BWA for the alignment. The situation is quite consistent in all my samples: always the forward reads are poorly mapped.

Does anyone have an explanation?

Many thanks
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