Illumina Genome Analyzer - Single End Vs Paired End

Question

[Bio_X2Y]

From a machine/protocol perspective, how are paired-end reads treated differently from single-end reads by the Illumina Genome Analyzer?

My background isn't in biology, so I find the documentation a little difficult to follow.

In particular, I'm interested in the following:

• Are two separate clusters generated on the same flowcell for each fragment, one corresponding to each end?
• Are two sets of images output by the system, one for each end?
• Where does the Illumina Paired-End Module fit in? Is it used to generate the clusters differently, or does it have something to do with the imaging?

I am happy to split these into separate questions if people feel they cover too many topics, although I suspect an explanation might cover them all.

Answer 1

[Rm]

"paired ends" refers to the two ends of the same DNA molecule.

• http://en.wikipedia.org/wiki/Paired-end_Tags
• http://seqanswers.com/forums/showthread.php?t=503
• http://seqanswers.com/forums/showthread.php?t=21
• http://www.illumina.com/documents/seminars/presentations/2010-06_sq_02_lakdawalla_compedium_genomic.pdf
• The Paired-End Module is a fluidics station that attaches to the Genome Analyzer. After resysthesis of the reverse strand, the original forward strand is cleaved away and the complementary strands are bridge amplified to form new clusters for the second read.

Answer 2

[ofanoyi]

http://thegenomefactory.blogspot.com/2013/08/paired-end-read-confusion-library.html

This post explained well as far as I can tell.