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Search: Posts Made By: Nitrogen-DNE-sulfer
Forum: Illumina/Solexa 02-12-2013, 08:49 AM
Replies: 31
Views: 14,463
Its just happy mapping with nextera. dilute...

Its just happy mapping with nextera.

dilute DNA to LMOI (5% of genome per well)...Make Nextera Libraries with specific barcode pair per well. All fragments with that barcode can be assumed to be...
Forum: Illumina/Solexa 11-02-2012, 11:34 AM
Replies: 2
Views: 2,448
Any one figure out how to hack the RFIDs?...

Any one figure out how to hack the RFIDs? Thinking of pooling the scraps of runs which fail to cluster.
Forum: Illumina/Solexa 11-02-2012, 11:29 AM
Replies: 13
Views: 9,939
Any had luck hacking the RFID system? I dont...

Any had luck hacking the RFID system?
I dont see any mention of it in the recipe XML files
Forum: Ion Torrent 08-21-2012, 07:19 AM
Replies: 10
Views: 10,603
Has anyone tried to move the Ampliseq to MiSeqs?...

Has anyone tried to move the Ampliseq to MiSeqs? 48 genes for TruSeq seems a bit limiting.
Forum: Illumina/Solexa 08-17-2012, 07:56 AM
Replies: 18
Views: 6,210
Any tricks for avoiding the massive library...

Any tricks for avoiding the massive library dilutions steps on the MiSeq. The neutralization seems like an excessive dilution which could be done with more concentrated HCl? We're having to amplify...
Forum: Ion Torrent 05-09-2012, 02:27 PM
Replies: 121
Views: 99,862
Can anyone comment on the strand specific error...

Can anyone comment on the strand specific error specific to the PGM? Has this improved with their latest data release? Can you point to data where the Homopolymer data is better than 454? Its not in...
Forum: Ion Torrent 05-05-2012, 06:40 AM
Replies: 121
Views: 99,862
Its a good paper and I'll throw my unsolicited...

Its a good paper and I'll throw my unsolicited recommendations on there as well. I think Nick was generous with the Ion platform. The Library prep, EmPCR and CAFIE correction CPU time after the run...
Forum: General 05-05-2012, 05:46 AM
Replies: 39
Views: 22,065
Great paper Nick. Does anyone have experience...

Great paper Nick. Does anyone have experience with Low Amplification libraries on the MiSeq? Their protocol demands 10ul of library be diluted into 1ml of HT1 and this is further diluted 2:1 before...
Forum: Illumina/Solexa 05-19-2010, 11:53 AM
Replies: 13
Views: 5,942
GC Bias in ILMN 75mers

We see a similar effect with ILMN 75mers on GAIIx. Also done through a service provider with Human DNA.
DNA sheared with a Covaris and run on SOLiD shows a different effect so I dont think its your...
Forum: SOLiD 03-19-2010, 09:10 AM
Replies: 36
Sticky: SOLiD Adapters
Views: 34,511
I saw a slide at AGBT which suggested AB is...

I saw a slide at AGBT which suggested AB is making sequencing primers to allow customers to sequence their ILMN libraries on SOLiD. These would leverage the Y adaptors.
Speaking to the Invitrogen...
Forum: RNA Sequencing 03-01-2010, 07:06 AM
Replies: 19
Views: 8,758
I concure. I know of 4-5 labs now that have...

I concure. I know of 4-5 labs now that have tested RNAseIII vs chemical cleavage in SOLiD WT and the chemical cleavage is far more uniform. Other biases could be the A-tail step (if this is polyA not...
Forum: SOLiD 03-01-2010, 05:50 AM
Replies: 12
Views: 4,855
I'm very impressed with BFAST as its very clear...

I'm very impressed with BFAST as its very clear and published on what its doing. Well documented as well.
Maxmappers seed and extend is fast but appears to be a little messy in low complexity...
Forum: SOLiD 02-15-2010, 08:50 AM
Replies: 42
Views: 13,517
I was told it was a hexamer but one of the colors...

I was told it was a hexamer but one of the colors accounts for the vector to insert color. Not certain that clarifies anything but it may support the depletion story a bit more (ie 4096 as opposed to...
Forum: Helicos / Direct Genomics 12-14-2009, 12:58 PM
Replies: 17
Views: 9,973
I'd caution that paper in particular. Look at...

I'd caution that paper in particular.
Look at the GC bias they show on the ILMN. That's a pretty sloppy ILMN run and if you look at the supplement you can see they amplified the library AND used...
Forum: SOLiD 11-28-2009, 02:37 PM
Replies: 42
Views: 13,517
The 3' end error is from the random hexamers...

The 3' end error is from the random hexamers priming the cDNA synthesis and should not be seen on the 5' ends (of the template not the growing strand). I suspect an alignment issue is confusing the...
Forum: Sample Prep / Library Generation 11-23-2009, 04:43 PM
Replies: 27
Views: 10,147
One can design assays for DNA damage using...

One can design assays for DNA damage using enzymes which target it and exploit the products the enzymes create. We've used antibodies to 8-oxoG to measure photo damage on arrays and it lights up like...
Forum: Helicos / Direct Genomics 11-22-2009, 05:25 PM
Replies: 17
Views: 9,973
I tend to worry more about the esoteric enzymes...

I tend to worry more about the esoteric enzymes used in next gen which are still in the 1980s in terms of their understanding or publication record and Taq is not one of them.

PCR is a far more...
Forum: Sample Prep / Library Generation 11-18-2009, 06:24 AM
Replies: 27
Views: 10,147
Yes, Pairs are always better to measure start...

Yes, Pairs are always better to measure start points and distinct molecules but with single ended reads we just assume if any single replicated start point is identical it was PCR induced. This is...
Forum: Sample Prep / Library Generation 11-17-2009, 05:50 PM
Replies: 27
Views: 10,147
Great Thread, Stepping back a bit to dissect...

Great Thread,

Stepping back a bit to dissect this we have been testing how far we can go with simpler Fragment libraries as a first measure of this. Most Circularized protocols have many...
Forum: Sample Prep / Library Generation 08-20-2009, 11:33 PM
Replies: 3
Views: 8,037
It should work with 454 we've done this on...

It should work with 454
we've done this on SOLiD as the amines block T4 DNA ligase so the ends can't ligate to the adaptors.
I'm curious if the 600bp insert size holds on other platforms?
Any...
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