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Old 04-24-2009, 08:58 PM   #2
Nils Homer
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Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285

Originally Posted by totalnew View Post
Hello, all

I am completely new in bioinformatics, I start to read papers about alignment, but I just couldn't make an image how paired-end alignment works. I'v been searching around by google, it seems I couldn't get a tutorial or paper to clearly instruct me that.

What I need is a tutorial with some simple examples of PE alignment. Can anyone provide me a link here? Thanks a lot.
Check out papers for aligners like MAQ or SOAP. Most aligners align each end independently, or at most consider using one end and the expected insert size to infer the location of the other (to be more sensitive).
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