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Old 04-27-2009, 01:15 PM   #7
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Location: Boston

Join Date: Feb 2008
Posts: 693

On the contrary, my experience is detecting structural variations (SVs) particularly presses for highly effective pairing. In the real world, abnormal pairs are most likely to be caused by false alignments rather than true SVs, which is also true for cancer genomes. And if a read can be paired with its mate, the alignment tends to be correct. I know several groups on detecting SVs put a lot of effort on getting more reads paired.

Whether keeping all hits is a debate. Surely we can recover anything, but the cost is considerable. How to use them effectively for SV detection is also an open question, I think. In addition, for effective pairing, keeping thousands of hits or keeping equally best hits only is not good enough. It is important to see sufficient suboptimal hits. NovoAlign is the most accurate aligner mainly because it sees many suboptimal hits and achieves highest pairing fraction.

Alignment accuracy is no so important for resequencing, but it is one of the most important factors for SV detection.

Last edited by lh3; 04-27-2009 at 01:20 PM.
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