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Old 06-03-2013, 04:01 AM   #1
Nullie
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Default mapping advantages

Is there an advantage to mapping using single end reads over paired end reads? or the other way around?
will there be a difference in the accuracy of the mapping between the two options?

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Old 06-03-2013, 04:38 AM   #2
dpryan
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In general, paired-end reads will produce better mappings, simply due to the fact that one read can act as an anchor for its mate, should the mate map equally well to multiple places.
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Old 06-03-2013, 10:59 AM   #3
Nullie
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Are there more advantages to PE over SE?
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Old 06-03-2013, 11:29 AM   #4
dpryan
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Quote:
Originally Posted by Nullie View Post
Are there more advantages to PE over SE?
There can be, it depends on what your goals are.
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Old 06-03-2013, 11:32 AM   #5
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Paired end reads should be your preference if doing any splice variation analysis as they will define transcript boundaries with much greater confidence than single end reads will.

If all you are concerned with is differential gene expression, its really a wash in my mind - either will give you essentially equally good data. In that case, the difference comes down mainly to cost.
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Old 06-03-2013, 01:02 PM   #6
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Quote:
Originally Posted by dpryan View Post
There can be, it depends on what your goals are.
If I dont have a reference genome to map against which should I use?
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