High Short Reads %

[elly]

Hello, there,,

Recently, I perfomed the GS FLX Sequencing run using 70X75 PTP, 4 Regions Gasket.
Unfortunately, I got some weired results.
Actual keypass reads# of my library was about ~170000, but most of them(~70%) were filtered out due to short read length. Control reads were also similar results.
This is the first time that I get this kind of problem while I'm using 454's Genome sequencer.
I'm supspecting of reagent itself or instrument fluidic part.

Is there anyone who can hlep me or suffering from this kind of issue?

[glacerda]

I have no idea of what is causing it, but short read lengths are typical of multiple templates in a bead. When this occurs, the sequence quality drops and the read is trimmed and is discarded or becomes short.

[kmcarr]

Multiple templates per bead results in mixed reads, not short reads. That would also not explain the results with the control reads. Given that you saw the problem with the control samples focus your search on the sequencing run itself (as opposed to the library preparation or emPCR). Contact Roche support with and include information about the lot number(s) for the sequencing kit.