[GenoMax]

Anyone tried it yet? How does it work compared to hard coding?

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Phillip

We did not see any major differences in new RTA and hard-coded matrix (using 2 separate MiSeq's where that was the only difference among the two machines).

We have not installed the release version located at the link posted but I believe it has the same RTA code we tested.

[GenoMax]

Where did you find the info about not lowering cluster density and only using a 5% phiX spike? I'd be really reluctant to test this on someone's sample! I have a RADseq library coming up that has some in-line indices that were poorly designed/chosen together with the problem that all the inserts start and end with the same restriction digest sites.

That will be the standard recommendation from Illumina. You can confirm with your local FAS.
If you have a sample that is known to be strange then deliberate under loading may be the safer route to take.

[mcnelson.phd]

I'm a few days late responding to all of this, but I can also confirm that the new RTA software is working magic like you won't believe.

So far I've done two amplicon runs, both with only 2% phiX and both clustered around 1K/mm2 (one was actually at 1.2K) and the results are pretty amazing given the initial problems that were occurring. Obviously with cluster densities as high as I used, our PF rate was down around 75%, but that's still within Illumina's spec for just phiX so I can't complain. The reads themselves are very good, with only the last 75 bases of R2 really dropping below Q30, which is pretty typical overall for R2.

We've also done a genome run for some really high GC bacteria that we previously had lots of problems with even when using 30% phiX. This newest run was done with 5% and the results were so much better than before.

All in all, Illumina may have shot themselves in the foot a few months ago when they didn't test their RTA upgrade after the 2x250 upgrade, but now it's like they've replaced it with a bionic foot that will allow them to kick Life even harder in the you know what...