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03-02-2009, 01:22 PM
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#1 |
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Junior Member
Location: Miami Join Date: Feb 2009
Posts: 8
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why is paired-end alignment support so important
Is it because that if a read includes a paired-end, it is not easily to be found out by the current software? but why?
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03-03-2009, 08:05 AM
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#2 | |
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Rick Westerman
Location: Purdue University, Indiana, USA Join Date: Jun 2008
Posts: 1,104
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Quote:
(A) Yes, of course pair end alignment support is important. One can get more the double the information from paired ends -- e.g., the reads themselves plus the distance between them. Chaison & Pavner have an interesting paper in Genome Research commenting on the importance of paired ends. (B) While I suspect some alignment programs do not have paired end support it is hardly missing from many packages. It has been around The Roche-provided 'newbler' program does pair-end assembly. The ABI-provided 'corona' program does paired-end matching to a reference. That latter is not assembly per se but then the ABI SOLiD is not designed for de-novo assembly because of the short read lengths. Perhaps your question more revolves around assembly of very short reads? Or perhaps your question revolves around the mis-assembly due to repeat regions? In any case please restate your question more coherently. |
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