Titanium PE yields?

[anar]

Hi,

Our local sequencing provider says the soon-to-be-released Titanium PE kits produce a mix (about half-half) of shotgun reads and PE reads on a given run, where the shotgun reads come from the non-adapted ("internal") part of the circularised molecule. The only info I've seen on 454 Titanium PE sequencing is this ad from Roche: http://www.454.com/downloads/DeNovoC...omes_Flyer.pdf

• Does anyone know how many shotgun and/or PE reads one expects to get from a single plate of Titanium PE sequencing?
• Can anyone clarify whether there is a selection step for PE constructs prior to sequencing - if so why are non-PE shotgun sequences still prevalent?

Thanks!
Anar

[xiaowei]

In my opinion, the yield may be little lower, cause there are about 40nt linker exist in the PE reads. But I don't have the exact data.

For your question 2, I'm also puzzled. The estimation is quite depending on your sequencing DNA genome size. For larger genome, the two kinds of reads should be mixed to help get a de novo sequencing genome. For smaller genome, either reads will fix the genome, but the shotgun reads is much cheaper.