[pmiguel]

At the moment, 150pb read are not supported by Illumina on the Hiseq2000.
I think it's still possible to run it on the machine but there is a strong probability that your error rate explode at the end of the read. And I don't think it will be suitable for your application.
Unofficially, our FSE told us that a "correct" error rate for a 100nt read was below 2% (I think it was V2 kits a that time, it may have vary with V3 kits). I won't be surprise if your reach 4 to 5% error rate with a 150nt read.

Here is a plot of the error rate (phiX) for our most recent HiSeq2000 run:



Just for the top surface. Bubbles drive the error rate up higher for the bottom surface. Even so the error rate at 100 bases is generally below 0.5%.

The Sequence Analysis Viewer (SAV) shows >80% of the reads with no errors (counting both surfaces). Again, this is based on aligning phiX reads spiked into 7 lanes of the flowcell to phiX by the instrument software.

--
Phillip

[huguesparri]

I've checked our last 2*100nt run. On the PhiX control lane, error rate is between 0.8 and 1%. But for the spiked PhiX in our sample, it's just above 1%.
:'(

[JackieBadger]

MiSeq is now capable of 2x250b PE

[NextGenSeq]

Also the upgraded MiSeq gives 16 million reads.

[snetmcom]

Also the upgraded MiSeq gives 16 million reads.

16million clusters or reads?

[JackieBadger]

Reads....there are many more clusters... Without the upgrade MiSeq produces up to 5 million reads.

[kmcarr]

Reads....there are many more clusters... Without the upgrade MiSeq produces up to 5 million reads.

No, with the upgrade the output is 15-17 million CLUSTERS. This makes 30-34 million PE reads.

[trauba]

What exactly is it that limits the read length anyways?
I understand imperfect cleavage of fluorescence reduces the # of extending oligos, lowering the signal + adding noise.
Also, eventually some oligos get "out of phase" and then muddy the signal. Is this somewhat caused by insufficient purging of reagents from previous cycles?

Thanks.
Jim