paired end sequencing - direct/incerted repeats

[bbjdy]

Hi all,

Doe anyone have experience with nextgen sequencing of BACs containing large direct and inverted repeats? Which technology (454 or solexa, using resp. emulsion-PCR on beads and brigde-PCR on solid phase) would be most suitable for this?
how long can you go for a paired end library on 454 or Solexa (I know with 454 there is a kit for 3K long-tag paired end sequencing)? And what is the accuracy of library length (e.g. 3 Kb +- 100? bp)?
Any help on this is welcome! Thanks,

Jurgen

[mchaisso]

One possible approach if the coverage is high enough is to simply look for breakpoints that are sequenced (repeat junctions, etc).