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Search: Posts Made By: ikripp
Forum: General 05-27-2019, 09:17 PM
Replies: 6
Views: 1,611
Posted By ikripp
I would suggest doing a trial on a ladder with...

I would suggest doing a trial on a ladder with intervals as shown in the image, different brands cut at different ratios so trialling the product in house has always been our best approach.
Forum: Sample Prep / Library Generation 05-15-2019, 03:12 PM
Replies: 6
Views: 950
Posted By ikripp
Our workflow uses the Agilent tapestation to...

Our workflow uses the Agilent tapestation to quantify the PCR products which are then normalised from this and pooled as required. There are some limitations to the accuracy of this method but...
Forum: Illumina/Solexa 04-14-2019, 08:03 PM
Replies: 1
Views: 542
Posted By ikripp
PhiX is the control spike in from Illumina, which...

PhiX is the control spike in from Illumina, which you can order from them. It is recommended for use with low diversity libraries and is added following the library denature and dilution. More info...
Forum: Sample Prep / Library Generation 12-04-2018, 06:23 PM
Replies: 11
Views: 3,569
Posted By ikripp
I had a meeting with our Qiagen rep recently who...

I had a meeting with our Qiagen rep recently who indicated that they may be working on a bacterial rRNA removal kit.

Definitely hoping to find a suitable alternative!
Forum: Illumina/Solexa 09-24-2018, 05:18 PM
Replies: 7
Views: 1,255
Posted By ikripp
Do you have access to the basespace account that...

Do you have access to the basespace account that this was run on? I'd be curious to see what the metrics tab looks like.
Forum: Sample Prep / Library Generation 09-23-2018, 03:34 PM
Replies: 2
Views: 1,408
Posted By ikripp
We do 1/5 reactions for Flex as we also did for...

We do 1/5 reactions for Flex as we also did for XT before changing over.
They appear to be comparable and we have had no issues.
Forum: Sample Prep / Library Generation 09-02-2018, 05:19 PM
Replies: 6
Views: 1,369
Posted By ikripp
We have decided to move from XT to Flex and have...

We have decided to move from XT to Flex and have found them comparable in cost and in output.
As Phillip suggested the XT index oligos work fine for flex, and I don't believe there is any...
Forum: Illumina/Solexa 08-28-2018, 05:24 PM
Replies: 15
Views: 5,640
Posted By ikripp
My experience with "best focus" issues is that it...

My experience with "best focus" issues is that it does come down to an over-clustered run, although we have a very over-clustered run on the machine at the moment and it hasn't failed - it just has...
Forum: Illumina/Solexa 08-16-2018, 07:58 PM
Replies: 3
Views: 2,845
Posted By ikripp
They ended up replacing the hard drive and that...

They ended up replacing the hard drive and that resolved the issue. I believe the pump error was a result of the hard drive failing. Tech support instructed me to power cycle the machine and when I...
Forum: Illumina/Solexa 07-25-2018, 04:51 PM
Replies: 14
Views: 1,570
Posted By ikripp
What did your library look like when you did the...

What did your library look like when you did the quant before you loaded it?
We find that if there are lots of small fragments they will preferentially cluster and produce poor quality results. I've...
Forum: Illumina/Solexa 07-19-2018, 08:08 PM
Replies: 0
Views: 1,274
Posted By ikripp
MiSeq network issues following maintenance

Has anyone had any issues with their MiSeq network connections following maintenance? This year we have had both the hard drive and the chiller replaced, and since then we have had issues of our...
Forum: General 06-12-2018, 07:12 PM
Replies: 1
Views: 1,707
Posted By ikripp
Post Is amplicon/16S sequencing a thing of the past?

I've been tossing up posting this for a little while, but decided, why not!

I work in a facility where we do 16S and shotgun metagenomics sequencing, and every now and then the idea that 16S...
Forum: Illumina/Solexa 06-10-2018, 03:55 PM
Replies: 2
Views: 720
Posted By ikripp
We have run libraries containing amplicons from...

We have run libraries containing amplicons from these primers, and I haven't seen any clustering issue related to them.

From my experience, the clustering of amplicons on the MiSeq is not linear,...
Forum: Sample Prep / Library Generation 05-30-2018, 03:21 PM
Replies: 1
Views: 740
Posted By ikripp
We have had success on the Chemagic using their...

We have had success on the Chemagic using their DNA Stool 360 protocol and the QIAamp PowerFecal protocol/kit on the QIAcube. Both of these work for 96 well plate throughput.

When we don't have...
Forum: Illumina/Solexa 05-13-2018, 07:23 PM
Replies: 15
Views: 5,640
Posted By ikripp
5pM made from the 20pM library as per Illumina...

5pM made from the 20pM library as per Illumina protocol.
Forum: Illumina/Solexa 05-13-2018, 05:28 PM
Replies: 15
Views: 5,640
Posted By ikripp
We do approximately a run each week and vary...

We do approximately a run each week and vary rarely do we have what is considered an unsuccessful run. I base the loading concentration off of the pool concentrations as determined by a HSD1000 tape...
Forum: Illumina/Solexa 05-10-2018, 05:13 PM
Replies: 3
Views: 2,845
Posted By ikripp
Update: Tech support have identified it as a...

Update:
Tech support have identified it as a software or hardware error and told me to power cycle.
Unfortunately its a hardware error so now I have an engineer coming to fix the machine.

Just...
Forum: Illumina/Solexa 05-07-2018, 05:37 PM
Replies: 3
Views: 2,845
Posted By ikripp
Post MiSeq Error in LanePump

Hi All,

We just ran a MiSeq 2x300bp amplicon sequencing run over the weekend and it has completed with decent specs but has shown an error that says the following:
"Error in LanePump. Syringe...
Forum: Illumina/Solexa 05-03-2018, 05:04 PM
Replies: 15
Views: 5,640
Posted By ikripp
I had the same issue - "Best focus too near edge...

I had the same issue - "Best focus too near edge of range" and after contacting tech support and being directed to run these tests:

Y Stage test
M3 mirror test
Z Stage test
Compensator test...
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