mapping advantages

[Nullie]

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?

Thank You!

[dpryan]

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.

[Nullie]

thank you

Are there more advantages to PE over SE?

[dpryan]

Are there more advantages to PE over SE?

There can be, it depends on what your goals are.

[mbblack]

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.

[Nullie]

There can be, it depends on what your goals are.

If I dont have a reference genome to map against which should I use?