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Forum: Illumina/Solexa 02-06-2019, 10:42 AM
Replies: 2
Views: 278
Posted By misterc
Load up the run with SAV and see what the...

Load up the run with SAV and see what the reported occupancy is. If it's below 90%, you've got too little library in there and need to increase the loading concentration. If it's 96% or higher,...
Forum: Illumina/Solexa 12-18-2018, 12:19 PM
Replies: 1
Views: 509
Posted By misterc
It likely has been discontinued already with...

It likely has been discontinued already with their release of NextSeq 550 like last year. Almost all the parts are identical, so you shouldn't have any problems getting service contract renewals,...
Forum: Illumina/Solexa 12-11-2018, 09:07 AM
Replies: 4
Views: 2,303
Posted By misterc
Yes, MiSeq should be in the same boat. If you...

Yes, MiSeq should be in the same boat. If you kill the run, it shouldn't write out to the RFID's so the cartridge and flow cell would still be useable. However, you'll have to change the recipe...
Forum: Illumina/Solexa 11-29-2018, 12:45 PM
Replies: 7
Views: 976
Posted By misterc
You could open it up and remove the internal USB...

You could open it up and remove the internal USB cable that passes through to the motherboard for the USB port on the right hand side of the instrument. I forget how the USB port on the back of the...
Forum: Illumina/Solexa 11-29-2018, 12:39 PM
Replies: 3
Views: 806
Posted By misterc
You can also use the NovaSeq XP workflow and load...

You can also use the NovaSeq XP workflow and load 4 different sample pools (1 pool per lane on an S4 flow cell) using the same 384 UDI adapters.
Forum: Illumina/Solexa 09-07-2018, 08:06 AM
Replies: 3
Views: 945
Posted By misterc
GSviral, you're correct on all statements there :)

GSviral, you're correct on all statements there :)
Forum: Illumina/Solexa 06-13-2018, 09:49 AM
Replies: 5
Views: 1,143
Posted By misterc
I'm curious if anyone else has had issues with...

I'm curious if anyone else has had issues with chipped glass wreaking havoc (instrument causes this with the FC loading mechanism being too forceful, and vacuum sucks these bits of glass into the...
Forum: Illumina/Solexa 06-12-2018, 10:08 AM
Replies: 5
Views: 1,143
Posted By misterc
Any NovaSeq user threads/sites out there?

Hi all,

With NovaSeq now 1 year old as a shipping platform, I'm curious if/where folks might be discussing their experiences with their NovaSeqs. Anything out there? I'm surprised there's little...
Forum: Illumina/Solexa 03-22-2018, 10:54 AM
Replies: 1
Views: 945
Posted By misterc
Yes, it's fine to do this.

Yes, it's fine to do this.
Forum: Illumina/Solexa 03-09-2018, 10:54 AM
Replies: 7
Views: 1,513
Posted By misterc
MiniSeq is essentially a single camera NextSeq,...

MiniSeq is essentially a single camera NextSeq, so 2-color SBS there (not 4).
Forum: Illumina/Solexa 01-22-2018, 10:24 AM
Replies: 23
Views: 5,883
Posted By misterc
http://enseqlopedia.com/2016/10/index-mis-assignme...

http://enseqlopedia.com/2016/10/index-mis-assignment-to-illuminas-phix-control/
Forum: Illumina/Solexa 01-18-2018, 03:29 PM
Replies: 6
Views: 928
Posted By misterc
Good point. Yes, it's the latter (separate...

Good point. Yes, it's the latter (separate syringes pull the fluid through each of the two lanes simultaneously). It's entirely possible thiNGS has a fluidics issue on lane 1 there, but it seems like...
Forum: Illumina/Solexa 01-18-2018, 02:31 PM
Replies: 6
Views: 928
Posted By misterc
NextSeq fluidics lane pairs are odd vs. even...

NextSeq fluidics lane pairs are odd vs. even (i.e. lanes 1 & 3 get SBS pumping while lanes 2 & 4 are imaged).
Forum: Illumina/Solexa 01-17-2018, 11:30 PM
Replies: 23
Views: 5,883
Posted By misterc
IIRC, James Hadfield wrote up a very nice article...

IIRC, James Hadfield wrote up a very nice article on enseqlopedia showing how PhiX reads can get mis-associated with sample index sequences (when using Illumina's non-indexed PhiX) on patterned flow...
Forum: Illumina/Solexa 01-08-2018, 08:48 AM
Replies: 2
Views: 443
Posted By misterc
Hi, Yes, you should be basing your...

Hi,

Yes, you should be basing your calculations by disregarding read 1. Illumina is essentially double-counting as you'll get 400M clusters per flow cell on a High Output kit (dependent on...
Forum: Illumina/Solexa 01-04-2018, 12:24 PM
Replies: 13
Views: 2,490
Posted By misterc
Cheaper instruments from the orange empire...

Cheaper instruments from the orange empire typically mean higher cost per sample. The other piece to Firefly is the module (shipping sometime later in 2018 IIRC) that can perform sample prep for this...
Forum: Illumina/Solexa 11-02-2017, 10:15 PM
Replies: 26
Views: 5,982
Posted By misterc
List price on S4 reagent kits is about $30K. For...

List price on S4 reagent kits is about $30K. For NovaSeq sites with ≥5 NovaSeq instruments, they're able to get a discount large enough to achieve the "20% cheaper than HiSeq X" statement Francis...
Forum: Illumina/Solexa 05-05-2017, 02:29 PM
Replies: 4
Views: 2,088
Posted By misterc
If you switch back to the 0.5% Tween + 0.03%...

If you switch back to the 0.5% Tween + 0.03% Proclin maintenance wash solution, be sure and rinse the NaOH from your lines. For good measure, I'd do two complete "maintenance wash" runs with just...
Forum: Illumina/Solexa 03-28-2017, 02:49 PM
Replies: 4
Views: 2,699
Posted By misterc
It does depend on library type as well as insert...

It does depend on library type as well as insert size. I usually get 350-400M reads passing filter per FC.
Forum: Illumina/Solexa 03-27-2017, 11:25 PM
Replies: 113
Views: 26,722
Posted By misterc
Is 150ul of a 1nM library what Illumina...

Is 150ul of a 1nM library what Illumina recommends for a single S2 flow cell?!?
Forum: Illumina/Solexa 03-22-2017, 12:55 PM
Replies: 113
Views: 26,722
Posted By misterc
Does anyone have even a lane's worth of these new...

Does anyone have even a lane's worth of these new .cbcl files from a NovaSeq? I'd like to test our bioinformatics pipeline with the new bcl2fastq converter v.2.19 that supports NovaSeq.
Forum: Illumina/Solexa 03-02-2017, 08:12 AM
Replies: 113
Views: 26,722
Posted By misterc
Brian, your hypothesis is reasonable as there is...

Brian, your hypothesis is reasonable as there is no other possibility to explain the duplicate rate. Not surprisingly, we see similar duplicates on HiSeq 4000, as this 'characteristic' of ExAmp isn't...
Forum: Illumina/Solexa 03-01-2017, 03:21 PM
Replies: 113
Views: 26,722
Posted By misterc
Couple things that have changed on this lately. ...

Couple things that have changed on this lately.

1 - S4 flow cells now slated to ship in Q3 this year.
2 - S4 reagent kits only being reduced to be 20% cheaper than HiSeq X if you buy 5 NovaSeq...
Forum: Illumina/Solexa 02-15-2017, 09:34 PM
Replies: 11
Views: 1,528
Posted By misterc
That looks about right to me for 300-500K/mm2 raw...

That looks about right to me for 300-500K/mm2 raw density (and NOT overclustered). Those intensities look reasonable to me too for cycle 1 given the MiSeq ramps up exposure on the cameras at each...
Forum: Illumina/Solexa 10-25-2016, 08:27 AM
Replies: 18
Views: 5,926
Posted By misterc
Hi Nauman, If your reagent lots are also the...

Hi Nauman,

If your reagent lots are also the same, then yes you should get very similar results.
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