Override key pass in case where rapid and general libraries put on same GS-J run

[DCOM]

Hi,

We accidentally mixed a rapid library prep library (key pass GACT) with a general amplicon library (key pass TCAG) on the same run on a GS-Junior using LibL chemistry.

The machine will only detect the rapid library prep sequences (key pass GACT) and as such discards all the general amplicon library sequences (key pass TCAG) as no key pass.

I'm aware that in the system software manual is states: DO NOT mix samples prepared with the Rapid Library protocol with ones prepared with the FLX Standard protocol in the SAME region of the PTP device.

I was just wondering whether or not it would be possible to rescue these other sequences in some way bioinformatically, perhaps to override the use of the GACT keypass in favour of the TCAG keypass.

[jimmybee]

Yes you are able to override GACT keypass but I know you have to do some significant editing of parameter files to do so. I have done it before, but unfortunately I've lost the information. The best bet is to contact your Roche 454 tech, as they do have a processes to extract these (albeit against their guidelines..)

[DCOM]

Thanks very much jimmybee, I'll contact them and see how it goes.