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Old 09-17-2009, 12:44 AM   #5
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 870

Originally Posted by nilshomer View Post
At my current state of thinking, using paired end constraints during mapping is a heuristic to make up for the fact you did not map each end sensitively enough.
I think that's an overgeneralisation. I don't believe that paired end mapping is a panacea, but there are certainly cases where it offers benefits in sensitivity over single end mapping.

You say that using paired end is a way to make up for inadequate initial mapping, but with shorter read lengths there are plenty of reads which could map exactly, with no mismatches at multiple locations in the genome. Even where these are within repeat regions you can find that there are only a small number of locations where this read could map then using a paired end will give you a mapped position where a single end would not.

Having said that, I'd actually argue that for mapping type applications (eg ChIP Seq) the benefit of paired end comes from the separation between ends. Repeated regions can stretch over many tens of bases so that increasing the length of a single end read provides diminishing returns in terms of mapping efficiency. Using shorter paired end reads with a greater separation between the ends will in many cases offer a greater chance of positioning a read since one end may have escaped the repetitive region.

Having said all this, I personally would stick with single end reads for ChIP-Seq, mRNA seq and similar applications from a cost point of view. We do a lot of paired end sequencing at our site but normally it's for applications which absolutely require it, such as 4C.
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