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Search: Posts Made By: razibus
Forum: Illumina/Solexa 02-13-2013, 01:11 PM
Replies: 13
Views: 3,739
Posted By razibus
A temperature of only 60-70C can dammage AT-rich...

A temperature of only 60-70C can dammage AT-rich DNA?
Forum: Illumina/Solexa 02-13-2013, 05:41 AM
Replies: 13
Views: 3,739
Posted By razibus
It's not a problem of quantitation. As I said...

It's not a problem of quantitation. As I said "I'm measuring the DNA concentration with Qubit." Nevertheless, you have to check your DNA is properly sonicated by using the bioanalyzer.

Anyway, I...
Forum: Illumina/Solexa 02-13-2013, 02:31 AM
Replies: 13
Views: 3,739
Posted By razibus
Thank you for your answer, it makes sense. Do you...

Thank you for your answer, it makes sense. Do you know that from your own experience or did you read a publication on the subject?

In the zymo kit, they recommend for larger DNA (>10 kb) to heat...
Forum: Illumina/Solexa 02-11-2013, 04:34 AM
Replies: 13
Views: 3,739
Posted By razibus
Thank you for your answer, it's very relevant. ...

Thank you for your answer, it's very relevant.

I tried Qiagen columns but also Zymo Research...
Forum: Illumina/Solexa 02-07-2013, 11:08 PM
Replies: 13
Views: 3,739
Posted By razibus
I tried sonicating at 5kb and 3kb. The sonication...

I tried sonicating at 5kb and 3kb. The sonication profile looks good on the bioanalyzer.

However, the amount of DNA before sonication and after sonication/purification is very different. Indeed,...
Forum: General 08-19-2011, 06:50 AM
Replies: 6
Views: 5,402
Posted By razibus
Primer-BLAST is quite nice but it is also slow...

Primer-BLAST is quite nice but it is also slow and you cannot do batch requests.

I tested Primer Z (http://genepipe.ngc.sinica.edu.tw/primerz/beginDesign.do) and RExPrimer...
Forum: General 08-18-2011, 06:37 AM
Replies: 6
Views: 5,402
Posted By razibus
primer design

I'm using Oligo 7 (http://www.oligo.net/) for designing primer but one of the weakness of this software is that you have to check for possible SNPs in the primers you get.

I'm trying to see if...
Forum: General 08-05-2011, 01:13 AM
Replies: 7
Views: 2,600
Posted By razibus
Very interesting. Where did you get the info? Did...

Very interesting. Where did you get the info? Did you read it in a recent paper?
Forum: General 08-04-2011, 03:06 AM
Replies: 7
Views: 2,600
Posted By razibus
If you get a high number of mutations to check,...

If you get a high number of mutations to check, it will be very costly and time-consuming to use Sanger Sequencing but if the number of mutations is reasonable then go with 3730.

As you stated, it...
Forum: Illumina/Solexa 07-22-2011, 08:28 AM
Replies: 74
Views: 49,183
Posted By razibus
Like James explained, Goldengate is a large...

Like James explained, Goldengate is a large platform which includes several technologies like primer design. This platform is also shared and used on other technologies from illumina, for example...
Forum: Illumina/Solexa 07-21-2011, 01:13 AM
Replies: 74
Views: 49,183
Posted By razibus
I think this service will be provided via...

I think this service will be provided via GoldenGate platform.
Forum: General 06-17-2011, 05:02 AM
Replies: 39
Views: 24,067
Posted By razibus
Thank you Mucku for this relevant answer. I...

Thank you Mucku for this relevant answer.

I did not notice my mistake and you are absolutely right : total output of GS Junior is 40Mb (specification from Roche) and it will be 80Mb at the...
Forum: General 06-16-2011, 11:23 PM
Replies: 39
Views: 24,067
Posted By razibus
As stated by Mr Robison, because of primers and...

As stated by Mr Robison, because of primers and specific key sequences your inserts can't be longer than 150bp.

Ion 316 chip is just available to order in Europe. Ion 318 Chip should be available...
Forum: General 06-16-2011, 02:55 AM
Replies: 39
Views: 24,067
Posted By razibus
I gave prices for europe only and as you know...

I gave prices for europe only and as you know prices are always higher here...

About PGM I can't remember if the run time is changed with 318 chip. Ask in PGM forum.

Whatever sequencer you...
Forum: Illumina/Solexa 06-16-2011, 02:42 AM
Replies: 0
Views: 905
Posted By razibus
heterogeneity of results

We are working on sequencing human exome using agilent for enrichment and GAIIx for sequencing.

We got a high heterogeneity of read profiles from a DNA sample to an other.

For example : for a...
Forum: Ion Torrent 05-31-2011, 01:21 AM
Replies: 1
Views: 3,125
Posted By razibus
Halo Genomics

I know there is already a topic here (http://seqanswers.com/forums/showthread.php?t=9378).

I also know they have protocols for ion torrent.

Does anybody have more details, or better a feedback?
Forum: Illumina/Solexa 05-24-2011, 01:39 AM
Replies: 3
Views: 4,456
Posted By razibus
Some information about TruSeq Custom Amplicon : ...

Some information about TruSeq Custom Amplicon :
- 85% success rate
- 10% design failure
- 5% PCR failure
- 2 weeks from orders to shipment
- QC kit will be available

And if I'm not mistaken,...
Forum: Illumina/Solexa 05-24-2011, 01:31 AM
Replies: 74
Views: 49,183
Posted By razibus
I have the exact information now : you can have 5...

I have the exact information now : you can have 5 runs of 6 GB on your MiSeq.
Forum: Illumina/Solexa 05-20-2011, 12:45 PM
Replies: 74
Views: 49,183
Posted By razibus
Ok, it was too easy. No comment. :p

Ok, it was too easy. No comment. :p
Forum: Illumina/Solexa 05-19-2011, 11:55 PM
Replies: 74
Views: 49,183
Posted By razibus
Sorry but I don't have the details, they told me...

Sorry but I don't have the details, they told me 10-15 runs. The device is not on the market so it is as hard to have information on MiSeq as to talk about PGM on this forum...

The main idea is...
Forum: Illumina/Solexa 05-19-2011, 07:12 AM
Replies: 74
Views: 49,183
Posted By razibus
You can have no more than 15 runs on the machine....

You can have no more than 15 runs on the machine. Keep in mind that you will have probably to buy a computer dedicated to the MiSeq.
Forum: General 05-19-2011, 07:04 AM
Replies: 39
Views: 24,067
Posted By razibus
- PGM : 2 hours (0.1 Gb) - MiSeq : 4 hours...

- PGM : 2 hours (0.1 Gb)
- MiSeq : 4 hours (1x35), 19 hours (2x100), 27 hours (2x150)
- GS Junior : 9 hours


These are just indicative prices :
- PGM : 78k€ and 820€ (316 and 318 chip) for the...
Forum: General 05-13-2011, 01:56 PM
Replies: 39
Views: 24,067
Posted By razibus
Thanks for your answer. So to your opinion :...

Thanks for your answer.

So to your opinion :
- if we want to buy one now, PGM seems to be the most relevant because of actual results and future evolution
- if we want to buy one at the end of...
Forum: General 05-13-2011, 07:27 AM
Replies: 39
Views: 24,067
Posted By razibus
We already tested some mutations by Sanger...

We already tested some mutations by Sanger sequencing but it's definitely not the fastest technique when you have a lot of mutations.

Maybe you are right and the 3 sequencers I asked for are not...
Forum: General 05-13-2011, 06:16 AM
Replies: 39
Views: 24,067
Posted By razibus
Ion Torrent vs MiSeq vs GS Junior

Hi,

We already sequenced several human exomes by using Illumina GAIIx. To confirm found mutations in complete families, we need a cheaper and faster sequencer.

Which sequencer is the best for...
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