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Old 09-12-2017, 01:07 PM   #3
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Location: Purdue University, West Lafayette, Indiana

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Originally Posted by r.rosati View Post
My two cents ... "It depends".
Balanced and you're doing WGS - you have the chance of picking the breakpoint within an intron, if it's not buried inside a repetitive element, but low coverage might hamper the call. You might have some more chances if you know what you're looking for, hence not relying solely on algorithms. Mate pair reads might help you.

EDIT: I'm re-reading it and I read like a fortune cookie. This is actually quite appropriate.
Would your answer change if the WGS coverage was 30X, instead of "low"?

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