SEQanswers

Go Back   SEQanswers > Search Forums

Showing results 1 to 19 of 19
Search took 0.00 seconds.
Search: Posts Made By: Number6
Forum: Illumina/Solexa 03-03-2017, 01:04 PM
Replies: 8
Views: 2,772
Posted By Number6
You can certainly streamline these library preps;...

You can certainly streamline these library preps; we do this for SNP genotyping at dozens or even hundreds of loci in up to 384 samples in a run, using tailed locus-specific primers and the 2-step...
Forum: Illumina/Solexa 01-10-2017, 08:52 AM
Replies: 113
Views: 43,277
Posted By Number6
the announcement from the JP Morgan Healthcare...

the announcement from the JP Morgan Healthcare conferene on GenomeWeb describes the NovaSeq as using the two color chemistry
Forum: Illumina/Solexa 04-18-2016, 10:23 AM
Replies: 0
Views: 1,383
Posted By Number6
Proclin in MiSeq washes?

Just curious, does anybody use Proclin in their maintenance wash for their Miseqs, like it's used in the washes for a HiSeq?
Forum: Illumina/Solexa 04-15-2016, 09:36 AM
Replies: 7
Views: 4,381
Posted By Number6
We typically run ~10% phiX for ddRAD libraries on...

We typically run ~10% phiX for ddRAD libraries on our HiSeq2500 running v4 chemistry, and they've been running fine. We typically see ~91% PF (%) at ~850 K/mm2 density, ~236 M Reads, ~215 M Reads PF,...
Forum: Illumina/Solexa 02-19-2016, 08:22 AM
Replies: 3
Views: 2,084
Posted By Number6
If it's multiple loci, we have a manuscript just...

If it's multiple loci, we have a manuscript just published online in Horticultural Research describing "AmpSeq," which works particularly well for SNP genotyping multiple loci. It's Yang et al.,...
Forum: Illumina/Solexa 01-30-2016, 07:36 AM
Replies: 22
Views: 6,254
Posted By Number6
Hi GenoMax, not in so many words, but they had...

Hi GenoMax, not in so many words, but they had reports of poor performance and the primary improvements in MCS 2.6 were for the Trusight Tumor 15 workflow, so rolling back was suggested if we weren't...
Forum: Illumina/Solexa 01-29-2016, 11:48 AM
Replies: 22
Views: 6,254
Posted By Number6
The upgrade was to MCS v2.6; we rolled back to...

The upgrade was to MCS v2.6; we rolled back to MCS v2.5
Forum: Illumina/Solexa 01-29-2016, 11:07 AM
Replies: 22
Views: 6,254
Posted By Number6
Did you upgrade the MiSeq software released...

Did you upgrade the MiSeq software released around the end of November last year? We did, and all low complexity library sequencing looked terrible. We rolled back the software and all has been fine...
Forum: Illumina/Solexa 06-15-2015, 09:46 AM
Replies: 2
Views: 3,608
Posted By Number6
Hi ADGM, if you're looking at the material after...

Hi ADGM, if you're looking at the material after the bead normalization, the eluted libraries are single-stranded DNA at this point. qPCR or dPCR can be used to quantify your libraries, but they...
Forum: Illumina/Solexa 05-29-2015, 02:19 PM
Replies: 1
Views: 1,492
Posted By Number6
We've been running a number of targeted SNP...

We've been running a number of targeted SNP genotyping projects, which are amplicon libraries based on Illumina's two-step PCR amplicon approach. Illumina has an app note. It uses Nextera tails on...
Forum: Illumina/Solexa 06-11-2014, 10:45 AM
Replies: 4
Views: 5,485
Posted By Number6
Thanks, nucacidhunter. This is the only time...

Thanks, nucacidhunter. This is the only time we've set up a titration to look at these, but we've noticed this occasionally with (our) PCR-free preps. Adding more DNA to the flowcell doesn't increase...
Forum: Illumina/Solexa 06-10-2014, 07:31 AM
Replies: 4
Views: 5,485
Posted By Number6
PCR-free clustering density issues?

Here are some observations for clustering density with PCR-free DNA preps, and I'm wondering if anyone else has observed the same? On several PCR-free preps, we run the samples at our usual...
Forum: Illumina/Solexa 07-23-2013, 07:15 AM
Replies: 10
Views: 3,625
Posted By Number6
If you have a custom primer for your sample, the...

If you have a custom primer for your sample, the MiSeq requires a higher Tm than primers on the HiSeq (I believe this is discussed in other threads in this forum). We had a sample that only sequenced...
Forum: Illumina/Solexa 06-21-2013, 11:39 AM
Replies: 75
Views: 37,647
Posted By Number6
Hi DaanV....you have come to this conclusion like...

Hi DaanV....you have come to this conclusion like many of us have. Digital PCR should do a much better job of quantifying the libraries. In fact, I've just ordered an instrument in the hope that it...
Forum: 454 Pyrosequencing 01-28-2013, 06:15 AM
Replies: 7
Views: 2,558
Posted By Number6
Hi Anthony, I did this a year or so ago, and the...

Hi Anthony, I did this a year or so ago, and the Fastx toolkit can do what you want. The barcode splitter in that toolkit puts the unmatched reads into a separate file. I have in my notes that the...
Forum: Illumina/Solexa 11-06-2012, 12:48 PM
Replies: 4
Views: 6,407
Posted By Number6
The MiSeq treats barcode reads differently than...

The MiSeq treats barcode reads differently than the HiSeq and one way to do this is to modify the MiSeq Reporter.exe.config file to include the "CreateFastqForIndexReads" setting. This is described...
Forum: Academic/Non-Profit Jobs 06-21-2011, 01:48 PM
Replies: 0
Views: 1,903
Posted By Number6
Associate Director, Genomics Facility

A Senior Research Associate position is available in the Genomics Facility of the Cornell University Life Sciences Core Laboratories Center (http://cores.lifesciences.cornell.edu). This position may...
Forum: Illumina/Solexa 06-02-2009, 09:16 AM
Replies: 6
Views: 3,187
Posted By Number6
Just some more observations: We recently had...

Just some more observations:

We recently had two runs in a row, on one of our two GAIIs that had very low intensity (first base average ~85). One was a PE flowcell (indexing) and the other a...
Forum: Illumina/Solexa 05-29-2009, 08:32 AM
Replies: 5
Views: 4,341
Posted By Number6
This probably won't make you feel any better, but...

This probably won't make you feel any better, but our IT group is already circling our two IPARs, waiting to scavenge......

Here are the specs:
8 x 3.16 GHz Cores
16GB RAM
3.4 TB usable storage...
Showing results 1 to 19 of 19

 

All times are GMT -8. The time now is 01:50 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO