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Forum: Illumina/Solexa 01-08-2019, 07:59 AM
Replies: 5
Views: 215
Posted By GW_OK
Might be due to the decrease in base diversity at...

Might be due to the decrease in base diversity at the beginning of the reads. Maybe you've got some primer dimer in there?
Forum: Illumina/Solexa 01-07-2019, 12:41 PM
Replies: 5
Views: 215
Posted By GW_OK
What'd the metrics graphs (intensity, %base,...

What'd the metrics graphs (intensity, %base, %Q30, error rate) look like?
Forum: Illumina/Solexa 12-13-2018, 11:41 AM
Replies: 1
Views: 391
Posted By GW_OK
Comparing A260 vs picogreen/Qubit should tell you...

Comparing A260 vs picogreen/Qubit should tell you if there's a large amount of ssDNA present.
Forum: Illumina/Solexa 11-08-2018, 08:47 AM
Replies: 1
Views: 801
Posted By GW_OK
I'm surprised you haven't had at least one visit...

I'm surprised you haven't had at least one visit from an FSE if this is a recurrent problem. How did you confirm that this was caused by bubbles?
Forum: Illumina/Solexa 11-08-2018, 08:39 AM
Replies: 8
Views: 1,370
Posted By GW_OK
One thing worth keeping in mind as well is the...

One thing worth keeping in mind as well is the difference in clustering chemistries between the two instruments. With the Nova using ExAmp and the Miseq using the "classic" bridge amplification the...
Forum: Service Providers 05-31-2018, 10:51 AM
Replies: 2
Views: 3,964
Posted By GW_OK
Hi Eric, We're CAP/CLIA and interested in...

Hi Eric,
We're CAP/CLIA and interested in collaborating.
Forum: Illumina/Solexa 04-06-2018, 01:24 PM
Replies: 13
Views: 1,294
Posted By GW_OK
If there's no mention of custom primers in the...

If there's no mention of custom primers in the sample sheet then that's not something to worry about.

My next thought would be to check the concentration of your NaOH. A heat denaturation attempt...
Forum: Illumina/Solexa 04-04-2018, 09:53 AM
Replies: 13
Views: 1,294
Posted By GW_OK
If you have a shift in peak size of ~125bp...

If you have a shift in peak size of ~125bp between your initial amplicon and the final library you make from it then it should have the appropriate adapters ligated to each end.

If your qPCR of...
Forum: Illumina/Solexa 03-26-2018, 12:25 PM
Replies: 22
Views: 1,907
Posted By GW_OK
Onboard diagnostics are in the "System Check"...

Onboard diagnostics are in the "System Check" icon under "Manage Instrument" from the main screen on the Miseq Control Software. The optics checks are fairly fast to run, the fluidics will take some...
Forum: Illumina/Solexa 03-26-2018, 11:58 AM
Replies: 22
Views: 1,907
Posted By GW_OK
What's troubling to me is that you don't have any...

What's troubling to me is that you don't have any intensity in read 2, which should always show if you have at least a read 1, regardless of index.

Have you run any of the onboard diagnostic...
Forum: Illumina/Solexa 03-26-2018, 11:09 AM
Replies: 22
Views: 1,907
Posted By GW_OK
That's intensity. I was talking about the graph...

That's intensity. I was talking about the graph that is from % Base, which is selectable in the menu from the gray button under Intensity.

Still, though, in looking at this graph it appears you...
Forum: Illumina/Solexa 03-26-2018, 10:48 AM
Replies: 22
Views: 1,907
Posted By GW_OK
Can you post the %base graph?

Can you post the %base graph?
Forum: Illumina/Solexa 03-19-2018, 07:34 AM
Replies: 7
Views: 1,756
Posted By GW_OK
It might be a thermal issue. Edit: But on...

It might be a thermal issue.

Edit: But on two different machines?
Forum: Illumina/Solexa 03-13-2018, 07:11 AM
Replies: 3
Views: 1,308
Posted By GW_OK
I do know Hiseq 2500's have two cameras. Here's a...

I do know Hiseq 2500's have two cameras. Here's a picture of the optical deck in case anyone is interested. You can see the green and red lasers at the left and top and the two cameras at angles on...
Forum: Illumina/Solexa 03-12-2018, 06:48 AM
Replies: 7
Views: 1,484
Posted By GW_OK
Good to know. I suppose the iSeq is single...

Good to know.

I suppose the iSeq is single color, since it's got the CMOS in the flowcell.
Forum: Illumina/Solexa 03-09-2018, 10:17 AM
Replies: 7
Views: 1,484
Posted By GW_OK
The lasers excite at fixed wavelengths. The...

The lasers excite at fixed wavelengths. The fluorophores emit at different respective wavelengths. The example given by kc3228 is for the dual color chemistries of the NextSeq and NovaSeq. The...
Forum: Illumina/Solexa 02-09-2018, 08:47 AM
Replies: 3
Views: 1,002
Posted By GW_OK
Well, yeah, but that's some serious capex burn.

Well, yeah, but that's some serious capex burn.
Forum: Sample Prep / Library Generation 02-09-2018, 07:43 AM
Replies: 2
Views: 969
Posted By GW_OK
Is there a reason you can't draw into a PAXgene...

Is there a reason you can't draw into a PAXgene tube?
Forum: Illumina/Solexa 02-09-2018, 07:17 AM
Replies: 3
Views: 1,002
Posted By GW_OK
Wow. I wonder who surplused $5M in...

Wow. I wonder who surplused $5M in instrumentation?
Forum: Illumina/Solexa 02-09-2018, 06:42 AM
Replies: 6
Views: 855
Posted By GW_OK
Custom primers have nothing to do with generation...

Custom primers have nothing to do with generation of clusters. Both ends of the library adapters must have the requisite P5 and P7 sites for proper bridge amplification on the flowcell.

And you...
Forum: Illumina/Solexa 02-08-2018, 11:54 AM
Replies: 6
Views: 855
Posted By GW_OK
But you can spike in custom primers, yeah? ...

But you can spike in custom primers, yeah?

And single read or paired-end, it doesn't really matter on the NextSeq? If it'll cluster you can just set it to do read 1.

We do single reads all the...
Forum: Illumina/Solexa 02-08-2018, 08:34 AM
Replies: 6
Views: 855
Posted By GW_OK
You mean a cBot? No, you can do single reads...

You mean a cBot?

No, you can do single reads on a NextSeq. I skimmed through the protocol and didn't see anything that made it cBot/Hiseq specific. Maybe I missed something?
Forum: Illumina/Solexa 01-09-2018, 09:42 AM
Replies: 13
Views: 2,391
Posted By GW_OK
I'll bet that's library prep costs, which is...

I'll bet that's library prep costs, which is inline with Nextera per sample costs.

Keith Robinson's saying the PE150 reagents are $625 with a 5% discount if bought in 4-packs.
Forum: Illumina/Solexa 01-09-2018, 06:51 AM
Replies: 13
Views: 2,391
Posted By GW_OK
One third of the reads for two-thirds the cost of...

One third of the reads for two-thirds the cost of a Miseq v2 kit. At least for PE150.

I really don't see the point unless they're trying to get installed in that last fraction of labs that just...
Forum: Illumina/Solexa 08-01-2017, 07:19 AM
Replies: 113
Views: 25,907
Posted By GW_OK
There've been a few hypotheses that ExAmp is...

There've been a few hypotheses that ExAmp is actually Recombinase Polymerase Amplification (RPA), developed by TwistDX.

Here's a Youtube video describing it (https://youtu.be/x6AbsOrSAoY?t=1m17s)...
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