Paper question

[genehunter2]

Hello everyone,

I just have a question about something I read on a paper(Burke et al 2010, 467, 587–590), which I dont quite understand...

This is from the methods

"Genome sequencing. DNA was extracted from 25 female flies collected from
each of the ACO1–ACO5 and CO1–CO5 populations and pooled within selection
treatments to make two Illumina paired-end libraries. We also created a library for the ACO1 replicate population only. The pooled libraries were each run on four (unpaired 54-bp) lanes of an Illumina Genome Analyser II, and the ACO1 library was run on a single (paired-end 36-bp) lane".

So the pooled samples, ACO1–ACO5 and CO1–CO5, were run using paired end... but below they say they were run in unpaired 54 bp lanes... so they were not paired end? btw paired end basically means they sequenced both strands... right?

TIA for your time!

Fred

Im completely new to these techniques, my only experience is with good old drhod sequencing. Im guessing this is obvious for most of you here, so I ask... can anyone point me to a accessible guide that explain how this Illumina NGS works?.

[simonandrews]

Paired end means that they would have sequenced a short stretch from either end of the fragments cloned in the library.

In this case it sounds like they used paired end adapters to create their library, but then ran these as a single end sequencing run. The paired end Illumina adapters are compatible with either a single or paired end sequencing run so many people (ourselves included) will generate a paired end library, even if they only intend to sequence one end. It means that you always have the option of doing paired end sequencing if you want to, and the cost of library production is the same in either case.