Control Lane - PhiX

[bioinfosm]

Hi,

We have been sincerely using the control lane in all our solexa runs thus far. The auto5 option for Solexa pipeline phasing, when control is in lane5, uses the control lane data to generate matrix and phasing on all other lanes.

I am curious as to what if we skip the control lane. The matrices anyways look pretty similar, and the slight changes we see in the control matrix as well, is ignored by the solexa rep

Anyone here tried looking into this? Any other alternatives to skip the control lane and still get some QC, meanwhile, taking advantage of one extra lane of another sample.

thanks..

[ScottC]

There's a few threads discussing the options for omitting the control lane. People from the Broad spike their samples with a mixture of DNA samples that, at each base position, read equally A, G, C and T. Other people don't use it at all if they're confident of the sample they're running. Illumina doesn't support any option other than the PhiX control lane, of course.

[bioinfosm]

Thanks Scott, but I am not sure what threads you refer to.

It is the option of 'not using the control lane at all, if confident of the sample' ... how do people prefer doing that, etc.

[ScottC]

Oh, actually on looking around a bit more, I think I've gotten confused as to the source of the information to which I was referring. It was posted on the Solexa google group...

http://groups.google.com.au/group/solexa/browse_frm/thread/de2a09a7a6ae503e/66763dd25f72bfb6?lnk=gst&q=phix#66763dd25f72bfb6

I have heard a few people mention that if they are re-sequencing, and they know the base composition of their sample, then the phiX lane isn't really required if the base composition around 50% GC.

Disclaimer: I'm just relaying what I've heard, and what I've seen written... I haven't tried any of the 'no PhiX control' methods!

Cheers,

Scott.