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Forum: Sanger/Dye Terminator 10-29-2018, 11:57 AM
Replies: 0
Views: 2,293
Posted By yaximik
SeqStudio users?

I wonder if anyone has information whether SeqStudio cathode buffer is the same as other running /cathode buffers for earlier ABI CE sequencers. In other words, can 10x running buffers for ABI CE...
Forum: Sanger/Dye Terminator 05-25-2017, 04:02 PM
Replies: 0
Views: 2,194
Posted By yaximik
SeqStudio

Anyone operated new SeqStudio? What are the operating costs?
Forum: 454 Pyrosequencing 05-19-2014, 03:58 AM
Replies: 0
Views: 2,190
Posted By yaximik
Picotiter plates

Doe anyone know what vendor manufactures Junior picotiter plates for Roche's 454?
Forum: Illumina/Solexa 03-27-2014, 01:04 PM
Replies: 44
Views: 17,962
Posted By yaximik
Addition of acetic acid likely will not, or very...

Addition of acetic acid likely will not, or very slightly may improve clustering above what is achieved with final NaOH at 1 mM. The mod was designed to take care of higher NaOH concentrations, which...
Forum: Bioinformatics 03-03-2014, 08:41 AM
Replies: 26
Views: 14,167
Posted By yaximik
I splurged and eventually purchased CLC GW...

I splurged and eventually purchased CLC GW subscription just to find that it is inferior to Geneious 6, at least in mapping reads to a reference. For both I used default settings when mapping MiSeq...
Forum: Illumina/Solexa 01-10-2014, 07:00 PM
Replies: 32
Views: 23,723
Posted By yaximik
Wow, if you can do 60 GB for about $4К - I am...

Wow, if you can do 60 GB for about $4К - I am your customer!
Forum: Illumina/Solexa 01-09-2014, 06:06 AM
Replies: 32
Views: 23,723
Posted By yaximik
I doubt it. Correct me if I am wrong, the...

I doubt it. Correct me if I am wrong, the hydraulic system is one for all lanes, so the same reagents (including primers) are going to all lanes. So different samples cannot be run at the same time,...
Forum: Illumina/Solexa 01-08-2014, 03:16 PM
Replies: 32
Views: 23,723
Posted By yaximik
Guys, you are asking a way to many questions in...

Guys, you are asking a way to many questions in making a project. All I need is to find the cist of sequencing of pre-made libraries on available instruments and compare available options (cost per...
Forum: Illumina/Solexa 01-08-2014, 03:02 PM
Replies: 32
Views: 23,723
Posted By yaximik
Wow, I was told that one cannot run a different...

Wow, I was told that one cannot run a different seqprimer on one lane in the HiSeq 2000 flow cell. That is an eye opener, how they do that.
Forum: Illumina/Solexa 01-08-2014, 02:57 PM
Replies: 32
Views: 23,723
Posted By yaximik
Well, that site does not provide the option I...

Well, that site does not provide the option I need, and when I tried to contact them by e-mail my request like went into a black hole. That sucks...

But the opp to get multiple quoting is...
Forum: Illumina/Solexa 01-08-2014, 09:19 AM
Replies: 32
Views: 23,723
Posted By yaximik
After looking through this thread I am still at...

After looking through this thread I am still at loss as to what is the cost of the entire run on 2500 or 2000. My problem is that my libraries have to be sequenced with my custom sequencing primers,...
Forum: Illumina/Solexa 12-13-2013, 06:39 AM
Replies: 44
Views: 17,962
Posted By yaximik
HCl is too strong acid I think, it will skew pH...

HCl is too strong acid I think, it will skew pH significantly. Obviously, one ul of 1M acetic acid is in excess to remaining NaOH, but it is much weaker and rather create acetate buffer.
Forum: Bioinformatics 11-15-2013, 11:32 AM
Replies: 50
Views: 14,027
Posted By yaximik
Thanks! I give it try.

Thanks! I give it try.
Forum: Bioinformatics 11-12-2013, 03:32 AM
Replies: 50
Views: 14,027
Posted By yaximik
I;d certainly try - can you post it?

I;d certainly try - can you post it?
Forum: Sample Prep / Library Generation 10-18-2013, 03:22 AM
Replies: 49
Views: 67,429
Posted By yaximik
Use TE with 0.05% Tween20 and set it to shake at...

Use TE with 0.05% Tween20 and set it to shake at 37. You may also need to sonicate it a bit to break clumps, but I would not do it if DNA was large
Forum: Illumina/Solexa 10-12-2013, 06:30 AM
Replies: 44
Views: 17,962
Posted By yaximik
In regard to eliminating effect of remaining NaOH...

In regard to eliminating effect of remaining NaOH I found a very simple solution. Make solution of 1M acetic acid in water, it perfectly stable on a bench. Add 1 ul to the final dilution of your...
Forum: 454 Pyrosequencing 09-25-2013, 02:07 PM
Replies: 11
Views: 5,954
Posted By yaximik
Well, on the other hand the same msg says they...

Well, on the other hand the same msg says they going to add longer reads to GS Jr etc., front-end procedure improvements (automatization?) - seem waste of efforts if GS JR is going to be dumped as...
Forum: Illumina/Solexa 09-24-2013, 04:30 AM
Replies: 44
Views: 17,962
Posted By yaximik
I stored original Illumina's aliquiot of 2N NaOH...

I stored original Illumina's aliquiot of 2N NaOH just on the bench, tightly closed, making single use 20 ul dilutions every time. Did not notice much difference after a year or so. Indeed, how much...
Forum: 454 Pyrosequencing 09-24-2013, 04:22 AM
Replies: 11
Views: 5,954
Posted By yaximik
I was usually provided access to their secure FTP...

I was usually provided access to their secure FTP on as needed basis, or the upgrade was sent on CDs. This time nothing like that, so this is why I wonder what is going on.
Please let me know what...
Forum: 454 Pyrosequencing 09-24-2013, 04:18 AM
Replies: 11
Views: 5,954
Posted By yaximik
Wow, no kidding... I wonder if the same is for GS...

Wow, no kidding... I wonder if the same is for GS Jr - I saw a few post here from GS Jr users about using 2.9 - I wonder how they got it. I am more interested in the analysis package though, as I was...
Forum: Illumina/Solexa 09-21-2013, 06:09 PM
Replies: 4
Views: 3,814
Posted By yaximik
All right, I did another run with the same...

All right, I did another run with the same library using the first protocol, but loaded the flow cell at ~33 pM instead of 25 pM as in the previous run. I got density up to 1144 with 85.2% PF as...
Forum: Bioinformatics 09-21-2013, 08:09 AM
Replies: 26
Views: 14,167
Posted By yaximik
Angry CLC workbench sucks ...

I took advantage of CLC's offer last spring to get a free 6 mo trial evaluation of full version of their Genomic Workbench. Now it is coming to end and I need a make decision whether it worth to pay...
Forum: Illumina/Solexa 09-21-2013, 07:04 AM
Replies: 4
Views: 3,814
Posted By yaximik
I found 2 protocols on library loading, which...

I found 2 protocols on library loading, which differ greatly in load ranges. One starts from 10 nM libraries and provides dilution tables from 20 pM to 50 pM final library concentrations - without...
Forum: 454 Pyrosequencing 09-21-2013, 06:45 AM
Replies: 11
Views: 5,954
Posted By yaximik
Is 454 nearly dead?

I wonder if others have the same frustrating experience as I do, which may be indicative of what I begin to suspect. 454 tech support was not quite forthcoming in the past, but at least I could get...
Forum: 454 Pyrosequencing 09-18-2013, 06:36 AM
Replies: 2
Views: 2,230
Posted By yaximik
Hey Nicole, I am trying to find 2.9 upgrade...

Hey Nicole,

I am trying to find 2.9 upgrade from GS Jr, but cannot. Can you please point me in right direction?
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