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Forum: Illumina/Solexa 03-19-2017, 02:04 PM
Replies: 6
Views: 1,689
Posted By barrmur
You should make sure the sequencing run is been...

You should make sure the sequencing run is been carried out with about 20% PhiX in order to increase the base diversity during the run. Sounds like the low diversity is leading to a number of the...
Forum: Illumina/Solexa 05-09-2016, 12:43 PM
Replies: 10
Views: 2,644
Posted By barrmur
Fully agree, just remember to account for the...

Fully agree, just remember to account for the lower amount of reads when using the v2 500 cycle kit as opposed to the v3 600 cycle kit.
Forum: Sample Prep / Library Generation 09-22-2015, 01:18 AM
Replies: 2
Views: 1,216
Posted By barrmur
Cheers, Had found that site but no specific...

Cheers,

Had found that site but no specific mention of NGS preps and always good to have confirmation it works ok. Anyone else on other NGS applications?
Forum: Sample Prep / Library Generation 09-21-2015, 07:13 AM
Replies: 2
Views: 1,216
Posted By barrmur
RNA Later - DNA Prep

Hi all,

Just wondering if anyone has ever used DNA isolated from cells that have been stored in RNA later for NGS, Metagenomics and methlylation analysis specifically?

I am assuming that the...
Forum: Illumina/Solexa 07-11-2015, 12:44 AM
Replies: 2
Views: 1,196
Posted By barrmur
Sorry but I don't think this is possible, at...

Sorry but I don't think this is possible, at least not from any area that user can access. It may be possible for tech support to help but may have trouble getting to them at the weekend. However if...
Forum: Sample Prep / Library Generation 06-18-2015, 02:49 PM
Replies: 18
Views: 16,520
Posted By barrmur
New tape station, 4200, to be released soon,...

New tape station, 4200, to be released soon, likely shipping in September. May be wise to wait and see what the offer is....

Looks like it will be capable of running 96 samples in "walk away" mode.
Forum: Illumina/Solexa 06-15-2015, 03:43 AM
Replies: 10
Views: 3,159
Posted By barrmur
Out of a matter on interest how many metagenomes...

Out of a matter on interest how many metagenomes do you intend putting on one lane? We are about to run some but I cannot seem to find a reliable answer as to how many reads are needed for good...
Forum: General 05-17-2014, 01:04 AM
Replies: 0
Views: 2,327
Posted By barrmur
Identify live cells only

Hi all,
Would welcome opinions on the following. I am trying to identify viable bacteria in solution after antimicrobials treatment to distinguish what has been killed and what has not. Dead...
Forum: Sample Prep / Library Generation 04-07-2014, 01:36 PM
Replies: 5
Views: 3,970
Posted By barrmur
Truseq pcr free libraries do run larger on a BA...

Truseq pcr free libraries do run larger on a BA due to the tailed adapters but I have not seen this before with nano libraries. One explanation my be incomplete mixing of the size selection beads...
Forum: Sample Prep / Library Generation 01-28-2014, 12:46 PM
Replies: 10
Views: 6,203
Posted By barrmur
Silly question first. Have you run them on the...

Silly question first. Have you run them on the chip a second time? It almost looks like bleed through from the ladder to be honest. Adapter concatamers is also possible but we have done a lot of chip...
Forum: Illumina/Solexa 09-10-2013, 12:56 AM
Replies: 19
Views: 6,942
Posted By barrmur
True the primers are pretty long (I think about...

True the primers are pretty long (I think about 20 each) and can be expensive but I guess you need to weigh up the benefits of a one step library prep over the longer protocol. If you have not seen...
Forum: Illumina/Solexa 09-09-2013, 03:00 PM
Replies: 19
Views: 6,942
Posted By barrmur
If you are thinking about gene specific pcr I...

If you are thinking about gene specific pcr I would include the illumina adapters and barcodes in the primers so you olmy need one pcr to create the libraries must like meta genomic preps. You will...
Forum: Illumina/Solexa 09-03-2013, 04:22 PM
Replies: 8
Views: 7,390
Posted By barrmur
See if you can get access to a fluidigm access...

See if you can get access to a fluidigm access array. You might be able to prep all of the samples on a single chip on the access array in a much quicker time than by hand.

You could otherwise try...
Forum: Illumina/Solexa 07-16-2013, 06:16 AM
Replies: 24
Views: 12,929
Posted By barrmur
What do you mean by failed? No clusters formed,...

What do you mean by failed? No clusters formed, low intensity data, fluidics check failed??
Forum: Illumina/Solexa 06-19-2013, 12:30 PM
Replies: 4
Views: 1,743
Posted By barrmur
Bear the following in mind however if you are...

Bear the following in mind however if you are performing a de novo on a miseq. Basespace/miseq reporter only samples 500Mb from each sample and tries to perform the assembly on this. If you have...
Forum: Illumina/Solexa 06-03-2013, 01:24 PM
Replies: 30
Views: 26,780
Posted By barrmur
Hmmm, puzzling alright. FYI some of our customers...

Hmmm, puzzling alright. FYI some of our customers have run chip sample without size selection and have gotten good results. I assume you are taking the tailed adapters into account when size...
Forum: Sample Prep / Library Generation 06-03-2013, 12:37 PM
Replies: 10
Views: 2,191
Posted By barrmur
You could use cDNA in the truseq prep but after...

You could use cDNA in the truseq prep but after fragmentation there might not be much left, depends on your input. Lots of people have used nextera sample preps. Lower sample input and no need to...
Forum: Sample Prep / Library Generation 06-03-2013, 12:34 PM
Replies: 2
Views: 2,174
Posted By barrmur
Easiest thing to do would be to dilute all your...

Easiest thing to do would be to dilute all your samples to a standard concentration and then pool equal amount accordingly. I have done this with 96 sample plenty of times. It takes time to do it but...
Forum: Illumina/Solexa 06-03-2013, 12:23 PM
Replies: 30
Views: 26,780
Posted By barrmur
17.2 seems really high. Our miseq performs really...

17.2 seems really high. Our miseq performs really well at 10pm giving us 10Gb plus for a 2 x 250 run. I guess most of the answers you will get will contain the question, " how did you quantify your...
Forum: Sample Prep / Library Generation 05-22-2013, 05:46 AM
Replies: 3
Views: 2,917
Posted By barrmur
Haloplex libraries

I have just completed a run of a FC using the Haloplex exome kit. While the protocol is nice and easy the cluster numbers are confusing me a bit. We quantified initially using the bioanalyzer and...
Forum: Illumina/Solexa 03-10-2012, 01:46 AM
Replies: 3
Views: 2,543
Posted By barrmur
As a add on, Is it possilbe to multiplex 8...

As a add on,

Is it possilbe to multiplex 8 mate pair libraries with 8 Nextera libraries on a HiSeq? If so what would be the best wat to go about it?
Forum: Sanger/Dye Terminator 09-27-2011, 12:29 PM
Replies: 5
Views: 4,821
Posted By barrmur
An old post I know but your problem is likely due...

An old post I know but your problem is likely due to the concentration of either your template or primers. If the template concentration is to high the primers are used up during cycle sequencing...
Forum: RNA Sequencing 10-13-2010, 01:44 AM
Replies: 2
Views: 1,988
Posted By barrmur
Nice idea, might give that a go. Cheers.

Nice idea, might give that a go. Cheers.
Forum: General 10-12-2010, 04:41 AM
Replies: 0
Views: 1,892
Posted By barrmur
Sequencing small DNA fragments (25bp)

Hi all,

Just wondering if anyone has any experience of the following. I want to sequence a single fragment of RNA to confirm it is what I think it is. Any suggestions on how to go about it. The...
Forum: RNA Sequencing 10-12-2010, 04:24 AM
Replies: 2
Views: 1,988
Posted By barrmur
Sequencing RNA

Hi all,

Just wondering if anyone has any experience of the following. I want to sequence a single fragment of RNA to confirm it is what I think it is. Any suggestions on how to go about it. The...
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