v3 Flowcells and Reagents?

[NextGenSeq]

Has anyone run the new v3 flowcells and reagents on the HiSeq2000? We need to purchase more reagents but I am hesitant to switch over without feed back from other people.

[dhinerfeld]

We haven't but will be soon. As I understand it, V3 will soon be the only option from Illumina. I actually have a question about how much library to load on the V3 kits to get in the range of 800k clusters/mm^2. On the V2 flow cells, we get about 600K with 9pm loaded. We titrated the load on the V2 lanes and the resulting cluster densities increased linearly with the load, to a point. In moving to a larger lane, I don't think the same would be true. Does anyone have experience with this?

[GW_OK]

We'll be transitioning to v3 soon as well. Our FAS suggested starting at 12pM.

[NextGenSeq]

Note the optics of your HiSeq have to be recalibrated before running v3 flowcells and reagents. The Y coordinates in the config file needs updating by using a beaded flow cell by your service engineer.

[GenoMax]

Something to make a note of: The quality table for the new, v3 kits has a range from “B” to “m" per Illumina tech support.

[pmiguel]

So now the highest quality value is 45? What was it previously?

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Phillip

[GenoMax]

So now the highest quality value is 45? What was it previously?

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Phillip

It was 40 (http://en.wikipedia.org/wiki/FASTQ_format).

[pmiguel]

Well the unavoidable cheap shot at Illumina is: kind of like having an amplifier that goes up to "11"?

Looks like the highest ordinal for a printable ascii char is "62" for "~". Roughly one error in 4 million base calls. For a 33 offset encoding you can reach a quality score of "93". One error in 8 trillion base calls.

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Phillip