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Search: Posts Made By: DNATECH
Forum: Bioinformatics 08-18-2017, 05:08 PM
Replies: 2
Views: 1,284
Posted By DNATECH
Local realignements are helpful not because of...

Local realignements are helpful not because of sequencing quality concerns, but because of the general difficulty to get alignments right around indels, especially towards the end of reads .
Btw,...
Forum: Illumina/Solexa 04-18-2017, 07:56 PM
Replies: 19
Views: 6,032
Posted By DNATECH
It shows that PCR-free libraries can hide a...

It shows that PCR-free libraries can hide a larger amount of adapters and adapter dimers somehow entangled in the y-adapters. We have several times seen surprises with (on the BA) clean looking...
Forum: Illumina/Solexa 04-13-2017, 08:21 AM
Replies: 19
Views: 6,032
Posted By DNATECH
nucacidhunter, this is definitely worth a try!...

nucacidhunter, this is definitely worth a try! (Is seemingly clean - according to BA - good enough?)

I agree SNPsaurus the problem is more complex.
Forum: Illumina/Solexa 04-12-2017, 09:33 AM
Replies: 19
Views: 6,032
Posted By DNATECH
It is great that the Biorxiv manuscript from the...

It is great that the Biorxiv manuscript from the Weissman lab has hopefully identified the cause of the problem which has been reported previously for some cases (the agent being "free barcoded...
Forum: Pacific Biosciences 11-11-2016, 11:15 AM
Replies: 2
Views: 2,713
Posted By DNATECH
Please see: ...

Please see:
http://dnatech.genomecenter.ucdavis.edu/2016/11/10/new-service-long-read-sequencing-on-the-pacbio-sequel/
Forum: Pacific Biosciences 11-11-2016, 10:51 AM
Replies: 21
Views: 6,230
Posted By DNATECH
Hi All, we have only run E.coli libraries with...

Hi All,
we have only run E.coli libraries with the new chemistry so far.
http://dnatech.genomecenter.ucdavis.edu/2016/11/10/new-service-long-read-sequencing-on-the-pacbio-sequel/
Forum: Vendor Forum 10-14-2016, 02:27 PM
Replies: 11
Views: 5,329
Posted By DNATECH
Do the kits come with adapters? If so how many...

Do the kits come with adapters? If so how many different barcodes?
Forum: Epigenetics 10-13-2016, 05:02 PM
Replies: 9
Views: 3,536
Posted By DNATECH
Hi clolalan, yes, somewhat similar fragment...

Hi clolalan,

yes, somewhat similar fragment lengths make the dosing much easier. RNA-seq libraries tend to be perfect.
Forum: Events / Conferences 09-26-2016, 06:55 PM
Replies: 0
Views: 1,123
Posted By DNATECH
RNA-seq workshop: Library Preparation and Introduction to Data Analysis; November

The UC Davis DNA Technologies (dnatech.genomecenter.ucdavis.edu) and Bioinformatics (http://bioinformatics.ucdavis.edu/) Cores would like to announce their autumn RNA-seq workshop:

RNA-Seq Library...
Forum: Epigenetics 05-30-2016, 12:30 PM
Replies: 9
Views: 3,536
Posted By DNATECH
Sequencing RRBS libraries (standard protocol) on...

Sequencing RRBS libraries (standard protocol) on the HiSeq 4000 has not been a problem for us - one has to dose in 30 to 40% of a balanced library though
Forum: RNA Sequencing 04-11-2016, 03:54 PM
Replies: 3
Views: 1,495
Posted By DNATECH
We do recommend our customers from South America...

We do recommend our customers from South America (shipments can be delayed quite often) to ship their RNA after samples after ethanol precipitation, pellets washed twice with 70% ethanol, and then...
Forum: Events / Conferences 04-11-2016, 03:39 PM
Replies: 0
Views: 1,268
Posted By DNATECH
RNA-seq Workshop at UC Davis; May 10th -12th

We would like to announce our coming RNA-seq workshop:
Library Preparation and Introduction to Data Analysis
This workshop is a collaboration of the DNA Technologies Core...
Forum: Academic/Non-Profit Jobs 01-25-2016, 09:56 AM
Replies: 0
Views: 536
Posted By DNATECH
Sequencing and Genotyping Project Leader -SRA IV

Hi All,

the DNA Technologies Core (http://dnatech.genomecenter.ucdavis.edu/) at UC Davis is looking for a new staff member to manage and run Illumina HiSeq sequencers, establish protocols on...
Forum: Illumina/Solexa 07-26-2015, 04:14 PM
Replies: 2
Views: 4,181
Posted By DNATECH
Please see post #23 in this thread:...

Please see post #23 in this thread: http://seqanswers.com/forums/showthread.php?p=172043#post172043
The Illumina patent is surprisingly readable.
Forum: Illumina/Solexa 05-20-2015, 11:30 PM
Replies: 53
Views: 70,559
Posted By DNATECH
Some HiSeq3000 data are analyzed in this thread: ...

Some HiSeq3000 data are analyzed in this thread:
http://seqanswers.com/forums/showthread.php?t=58353
Forum: Illumina/Solexa 05-20-2015, 11:24 PM
Replies: 22
Views: 13,103
Posted By DNATECH
The latest HiSeq3000 run (we did receive a few...

The latest HiSeq3000 run (we did receive a few flowcells) did average 378 million clusters passing filter, per lane. All libraries were size selected.

One obvious part of the exclusion...
Forum: Illumina/Solexa 05-11-2015, 03:15 PM
Replies: 22
Views: 13,103
Posted By DNATECH
Thanks a lot for the detailed analysis Brian. ...

Thanks a lot for the detailed analysis Brian.
Lutz
Forum: Illumina/Solexa 05-08-2015, 03:20 PM
Replies: 22
Views: 13,103
Posted By DNATECH
Hi Brian, Thanks for looking at the data. ...

Hi Brian,

Thanks for looking at the data. The files that I uploaded have 482,680,800 reads. The sequencer generates "reads" for each single nanowell - no matter if it is loaded or not. Thus,...
Forum: Illumina/Solexa 05-08-2015, 12:11 PM
Replies: 22
Views: 13,103
Posted By DNATECH
Hi Pmiguel, the basic procedure looks like: ...

Hi Pmiguel,

the basic procedure looks like:
- 5 ul of library (2 nM to 3 nM including PhiX)
- add 5 ul 0,1 N NaOH
- add 5 ul Tris (200mM)
- add 35 ul Enzyme Master Mix
- load all 50 ul onto...
Forum: Illumina/Solexa 05-08-2015, 10:37 AM
Replies: 22
Views: 13,103
Posted By DNATECH
Hi GenoMax, perhaps we are just being...

Hi GenoMax,

perhaps we are just being careful at the moment - since Illumina seems to be very careful and there is very little information so far. The customer samples (n=11) have been looking...
Forum: Illumina/Solexa 05-08-2015, 09:44 AM
Replies: 22
Views: 13,103
Posted By DNATECH
Hi Miguel, the input was 5ul of PhiX at 2...

Hi Miguel,

the input was 5ul of PhiX at 2 nM. So far we have used 2 nM concentrations for all our libraries/lanes. Illumina recommends up to 3 nM.
From what our FAS told us, I got the...
Forum: Illumina/Solexa 05-08-2015, 08:52 AM
Replies: 22
Views: 13,103
Posted By DNATECH
Yes, an average of 340 million clusters passing...

Yes, an average of 340 million clusters passing filter per lane.
Forum: Bioinformatics 05-08-2015, 08:47 AM
Replies: 6
Views: 2,303
Posted By DNATECH
Hi GenoMax, Thanks! Currently there are no...

Hi GenoMax,

Thanks! Currently there are no local duplicate metrics in the SAV viewer and no options in bcl2fastq for flagging or filtering for these cases.
People working with X Ten data get...
Forum: Illumina/Solexa 05-07-2015, 05:59 PM
Replies: 22
Views: 13,103
Posted By DNATECH
We are actually waiting for flow-cells for...

We are actually waiting for flow-cells for several weeks; I guess Illumina is surprised that anybody wants to use the new sequencers?
Forum: Bioinformatics 05-07-2015, 05:04 PM
Replies: 6
Views: 2,303
Posted By DNATECH
HiSeq3000/4000 duplicate removal

Hi All,

Our Illumina FAS mentioned that in underloaded lanes on the patterned flow-cells even PCR-free libraries can generate significant numbers of duplicates (clusters swapping over the "walls"...
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