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Old 07-18-2016, 03:52 PM   #5
KamilSJaron
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Location: Switzerland

Join Date: Apr 2016
Posts: 7
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You are right. Twice.

Mate-pair indeed should, be pointing out from each other, but this is not the problem. And here comes, why you were right twice - bowtie thought that I have pair-end reads, therefore he considered correct the fraction of reads close to each other pointing out to each other.

So when I have plotted histogram of insert sizes, I found that all correct reads (with flag 2) have very small insert size and those, which have small insert size and still do not have flag 2, they are pointing out from each other (mate-pair orientation) https://plus.google.com/u/0/10778698...81109861311357

So my ultimate explanation is, that I just have poorly prepossessed mate-pairs, because about half of them are in fact just pare-end reads (i.e. they probably just had trimmed adapter from one of the outer sides).
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