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Forum: Illumina/Solexa 02-26-2018, 02:06 AM
Replies: 2
Views: 2,662
Posted By Vinz
Most (if not all) systems/kits support both...

Most (if not all) systems/kits support both versions. At least MiSeq and HiSeq rapid run do. They come with a mix of primers. So it is your choice which system to pick. Both work.
Forum: Illumina/Solexa 02-17-2017, 01:25 AM
Replies: 8
Views: 2,192
Posted By Vinz
We are working on this. The current release...

We are working on this. The current release (3.27) contains 606 of those alleles.
However, we are not in favor of submitting partial sequence information for novel alleles. Therefore, we always...
Forum: Illumina/Solexa 02-16-2017, 04:05 AM
Replies: 8
Views: 2,192
Posted By Vinz
Our manuscript...

Our manuscript (http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3575-z) got published by BMC genomics. The peerageofscience experience was bumpy as currently there seems not to be a...
Forum: Oxford Nanopore 10-08-2016, 02:39 PM
Replies: 3
Views: 4,327
Posted By Vinz
10Gbases of useful data seems very, very much to...

10Gbases of useful data seems very, very much to me. We have not done runs in October. But we have so far not achieved more than 0.5Gbases (2D passed) even with R9.
ONT tends to confuse people by...
Forum: Illumina/Solexa 10-08-2016, 01:41 PM
Replies: 8
Views: 2,192
Posted By Vinz
Sorry, it is our first paper with...

Sorry, it is our first paper with peerageofscience and I am not yet familiar with the way to refer to manuscripts.
Keywords are: Next generation sequencing; HLA genotyping; high resolution, high...
Forum: Illumina/Solexa 10-07-2016, 08:42 AM
Replies: 8
Views: 2,192
Posted By Vinz
Interested in reviewing our manuscript on amplicon sequencing?

We started HLA genotyping by amplicon sequencing in 2013. 2.7 million samples and several thousand MiSeq/HiSeq runs later, we destilled some quite interesting lessons learned from the data.
Our...
Forum: Illumina/Solexa 02-02-2016, 11:23 PM
Replies: 6
Views: 4,057
Posted By Vinz
We target an annealing temperature of 60C.

We target an annealing temperature of 60C.
Forum: Sample Prep / Library Generation 01-27-2016, 08:33 AM
Replies: 13
Views: 3,216
Posted By Vinz
We published the indexing for 1536 samples in the...

We published the indexing for 1536 samples in the Supplementary of
this article in BMC Genomics (http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-63).
Forum: Illumina/Solexa 05-28-2015, 10:31 PM
Replies: 16
Views: 5,894
Posted By Vinz
Indeed the support usually stops thinking if...

Indeed the support usually stops thinking if cluster density is high. Our experience is that the MiSeqs are pretty robust with regard to overclustering and usually the problem lies elsewhere....
Forum: Illumina/Solexa 05-28-2015, 08:25 AM
Replies: 16
Views: 5,894
Posted By Vinz
Illumina currently has serious problems with...

Illumina currently has serious problems with MiSeq V2 and V3 reagents... Some lots perform terribly bad. Others are fine. It seems they are not communicating that well. I guess this is a problem...
Forum: Illumina/Solexa 05-28-2015, 08:14 AM
Replies: 8
Views: 2,076
Posted By Vinz
I hope the problem has been solved by now! ...

I hope the problem has been solved by now!
Anyway: With 2 native HS2500 we regularly get >300M cpf per flowcell and between 80 and 85% Q30 for amplicon data.
Forum: Illumina/Solexa 09-19-2014, 04:09 AM
Replies: 13
Views: 4,349
Posted By Vinz
The 2x250 rapid run kit for the HiSeq is supposed...

The 2x250 rapid run kit for the HiSeq is supposed to become available end of September. Just 2 weeks to go ...
Forum: Illumina/Solexa 05-19-2014, 12:09 AM
Replies: 21
Views: 14,972
Posted By Vinz
There was a timeout in the MiSeq software for...

There was a timeout in the MiSeq software for copying the fastq to the output folder. For V3 runs with many samples, copying stopped when exceeding this time. I think this was fixed with 2.4.1....
Forum: Illumina/Solexa 03-13-2014, 01:51 AM
Replies: 8
Views: 1,732
Posted By Vinz
And I guess you did put index information into...

And I guess you did put index information into your samplesheet. However, there was only one sample/one index sequenced. This should explain the pattern after 100 bases.
Forum: Illumina/Solexa 03-13-2014, 12:45 AM
Replies: 6
Views: 4,057
Posted By Vinz
We use not exactly the outer primers that...

We use not exactly the outer primers that Fluidigm recommends. We changed it to work with the generic MiSeq sequencing primers. Full description is published here...
Forum: Illumina/Solexa 03-12-2014, 01:00 AM
Replies: 6
Views: 4,057
Posted By Vinz
We use Fluidigm extensively for amplicon...

We use Fluidigm extensively for amplicon sequencing on the MiSeq. And I would be happy to share experiences regarding quality if you have more specific questions.
Key to success is to keep...
Forum: Illumina/Solexa 02-21-2014, 02:28 AM
Replies: 3
Views: 1,425
Posted By Vinz
Primerdimer/Short Product Bias on the MiSeq

Primerdimers are more efficient in cluster formation than longer products.
Our data suggests that the extent of this preference can be influenced by sample preparation after (!) cleanup. Anyone has...
Forum: Illumina/Solexa 02-20-2014, 11:58 PM
Replies: 50
Views: 37,394
Posted By Vinz
We have done up to 1536 multiplexing in a run so...

We have done up to 1536 multiplexing in a run so far. Demultiplexing by the MiSeq software worked well.
However, there is a bug in the current RTA version: There is a timeout for writing fastqs in...
Forum: Illumina/Solexa 01-15-2014, 03:47 AM
Replies: 17
Views: 13,496
Posted By Vinz
Thanks! Very interesting thoughts. Our...

Thanks! Very interesting thoughts.

Our impression is rather opposite of what you describe. We load 20% less on V3 and still get about 20% higher cluster densities. So in our hands V3 is more...
Forum: Illumina/Solexa 01-14-2014, 07:17 AM
Replies: 100
Views: 41,604
Posted By Vinz
It is not. I was told it would be released this...

It is not. I was told it would be released this year.
Forum: Illumina/Solexa 12-30-2013, 05:54 AM
Replies: 6
Views: 10,676
Posted By Vinz
Is this MiSeq or HiSeq data? Are you sure, the...

Is this MiSeq or HiSeq data?
Are you sure, the index was sequenced? If you do not specify it in the sample sheet, no index is sequenced. Then there is no way to determine the samples and split the...
Forum: Illumina/Solexa 09-16-2013, 05:57 AM
Replies: 5
Views: 2,386
Posted By Vinz
James covered the patterned flow cell in a recent...

James covered the patterned flow cell in a recent blog post (http://core-genomics.blogspot.de/2013/09/patterned-flowcells-what-can-we-expect.html). He is speculating about doubling the reads and >1Tb...
Forum: Illumina/Solexa 09-16-2013, 04:38 AM
Replies: 5
Views: 2,386
Posted By Vinz
Indeed we would need the throughput... We have a...

Indeed we would need the throughput... We have a couple of MiSeqs in operation.
Forum: Illumina/Solexa 09-16-2013, 04:02 AM
Replies: 5
Views: 2,386
Posted By Vinz
HiSeq2500 Read Length

When introducing the HiSeq2500 Illumina promised 2x250bp by 2nd half of 2013. On the specification page they still list 2x150pb. Anyone has information or experience regarding longer runs in rapid...
Forum: Illumina/Solexa 09-12-2013, 06:21 AM
Replies: 8
Views: 7,342
Posted By Vinz
If you optimize your PCR to give you reliable PCR...

If you optimize your PCR to give you reliable PCR products, you may skip normalization. With 15*75 amplicons you expect on average ~10000 reads (paired) per amplicon. That should be enough to get...
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