HiSeq2000 best run?

[pmiguel]

Again went high on the cluster density on several lanes:



Highest density was in lane 5:


But >95% of the clusters demultiplexed in lane 5. 273 million clusters passed filter. >87% of all the base calls and 93% of the base calls in pass filter reads were Q30 or higher.

(Actually lane 4 produced slightly more reads than lane 5.)

So, is that above spec, or is everyone using the most recent version of HCS getting results like this?

--
Phillip

[csquared]

It's definitely above spec but also an output that is quite reproducible if done carefully.

That said, just be sure you don't have any alignment issues. We have had similar runs and every once in a great while you can see some issues on alignment that were not obvious from the summary metrics. Very rare but worth looking for.

[GenoMax]

Are you looking to set a Guinness world record for the "most productive HiSeq lane ever"

I am not certain if you were to re-run this exact sample again you will be able to recreate this observation.

[NextGenSeq]

The MiSeq gives higher cluster densities and higher quality scores. Obviously fewer reads though.

[GW_OK]

Would you care to post library type, run length (looks like 2x100), other pertinent details?

[NextGenSeq]

On the MiSeq we routinely get over 90% of the reads with Q scores over 30. The last two runs were ChIP-Seq and SE50.

[pmiguel]

Would you care to post library type, run length (looks like 2x100), other pertinent details?

Lane 5 was a mixture of 7 different TruSeq DNA libraries. Whole genome shotgun for some bacterial, fungal and arabidopsis DNA preps. 2x101 plus a 7 nt. index read. Trying to think of other pertinent details...

Doesn't look like there were large-scale cluster misalignments -- at least the PE genome assemblies went well and I did not notice higher than normal disjoined pairs when mapping to a reference. (Thanks for that horrific image, though Csquared.)

--
Phillip

[RPiddock]

Our latest run had been great, HiSeq2000 but with a new camera type (apparently).

445.3GB is our predicted yield total for a 200 PE with index.

Lane 4 was our highest yeilding lane.