Difference in paired-end and single-end read ?

darshan · 09-30-2009, 10:14 AM

What is the difference and how does it work for illumina-solexa?

Thanks
Darshan

simonandrews · 10-01-2009, 12:44 AM

A library for an Illumina sequencer consists of a set of fragments of around 200-700bp with specific adapters ligated onto the ends. A basic single end run would use a primer to one of those adapters to sequence a short fragment (~30-100bp) from one end of the fragment. In a paired end run you can use a second primer to the other adapter to get a corresponding sequence from the other end of each fragment, thus you would end up with two sequences for every fragment, one from each end.

If you have paired end data you can therefore infer the full length of each fragment if you are mapping it back against a known reference sequence. You also have more information which can be used when mapping the sequence to the reference.

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09-30-2009, 10:14 AM	#1
darshan Junior Member Location: Durham NC Join Date: Sep 2009 Posts: 5	Difference in paired-end and single-end read ? What is the difference and how does it work for illumina-solexa? Thanks Darshan

10-01-2009, 12:44 AM	#2
simonandrews Simon Andrews Location: Babraham Inst, Cambridge, UK Join Date: May 2009 Posts: 871	A library for an Illumina sequencer consists of a set of fragments of around 200-700bp with specific adapters ligated onto the ends. A basic single end run would use a primer to one of those adapters to sequence a short fragment (~30-100bp) from one end of the fragment. In a paired end run you can use a second primer to the other adapter to get a corresponding sequence from the other end of each fragment, thus you would end up with two sequences for every fragment, one from each end. If you have paired end data you can therefore infer the full length of each fragment if you are mapping it back against a known reference sequence. You also have more information which can be used when mapping the sequence to the reference.