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Forum: Illumina/Solexa 11-01-2017, 04:44 AM
Replies: 1
Views: 278
Posted By ymc
Lower quality when number of reads is way higher than spec?

https://www.cnsi.ucsb.edu/sites/www.cnsi.ucsb.edu/files/facilities/ngs-faqs.pdf

According to UCSB, this is true for NextSeq. Is this the same for other machines?

If this is true, how do we deal...
Forum: Vendor Forum 10-29-2017, 11:27 PM
Replies: 106
Views: 40,884
Posted By ymc
Are there any updates for the current state of...

Are there any updates for the current state of nextseq? Is it still this bad or return to the good quality when v2 came out?
Forum: Oxford Nanopore 08-24-2017, 05:03 AM
Replies: 5
Views: 1,182
Posted By ymc
Thank you very much for your reply. I will go...

Thank you very much for your reply. I will go with the Basic pack then.
Forum: Oxford Nanopore 08-20-2017, 04:54 PM
Replies: 5
Views: 1,182
Posted By ymc
It seems like 1D^2 kit cannot be included in the...

It seems like 1D^2 kit cannot be included in the starter pack no matter what. Does that mean I have to order it separately?
Forum: Oxford Nanopore 08-20-2017, 04:37 PM
Replies: 5
Views: 1,182
Posted By ymc
Thank you very much for your reply. If I...

Thank you very much for your reply.

If I don't need the support, would it better to buy the Basic starter pack and then keep replenishing the sequencing kits and flowcells?

If I understand...
Forum: Oxford Nanopore 08-19-2017, 04:01 PM
Replies: 5
Views: 1,182
Posted By ymc
Merits of the $4,999 Enhanced Starter Pack?

The Basic one is only $1,000.
https://store.nanoporetech.com/minion/sets

Based on my understanding, if you user the wash kit, you can run the Basic pack 6 times and the Enhanced pack 12 times.
...
Forum: Oxford Nanopore 05-12-2017, 05:10 AM
Replies: 44
Views: 3,607
Posted By ymc
I am interested in working on samples with around...

I am interested in working on samples with around 10 human cells that share the same DNA (barring mosaicism). It will be great if you also give this scenario a try and tell us if we can get any...
Forum: Oxford Nanopore 05-11-2017, 05:12 PM
Replies: 4
Views: 1,106
Posted By ymc
Interesting, I am also doing something along the...

Interesting, I am also doing something along the line. Nevertheless, I am doing 16S DNA not RNA but presumably should be applicable to RNA. I have a hack specific to 16S that allows me to align R9...
Forum: Oxford Nanopore 05-11-2017, 05:44 AM
Replies: 44
Views: 3,607
Posted By ymc
Just curious. Is it possible to use Minion to...

Just curious. Is it possible to use Minion to sequence a single cell without any amplification at all?
Forum: Oxford Nanopore 05-08-2017, 05:28 PM
Replies: 4
Views: 1,106
Posted By ymc
oic. No wonder there were no follow-up to that...

oic. No wonder there were no follow-up to that Matt Loose paper.
Forum: Oxford Nanopore 04-27-2017, 08:30 PM
Replies: 4
Views: 1,106
Posted By ymc
Question about ONT's Developer Agreement

Anyone here signed ONT's Developer Agreement?

I read the fine terms. It seems like anything that built on top of their developer kit will become ONT's intellectual property. Is that...
Forum: Illumina/Solexa 01-15-2017, 07:42 PM
Replies: 113
Views: 18,136
Posted By ymc
Thanks for your reply. Then from the cost...

Thanks for your reply.

Then from the cost perspective, it is not that impressive.

Big jump is throughput is always welcomed by the big genome centers. However, if base accuracy is down due to...
Forum: Illumina/Solexa 01-14-2017, 06:46 AM
Replies: 113
Views: 18,136
Posted By ymc
Reagent cost is $6375 per flowcell for Hi Seq X....

Reagent cost is $6375 per flowcell for Hi Seq X. If the price of the new reagent is 80% of Hi Seq X, then it is $5100 per flowcell for NovaSeq 6000.

This means that the new reagent cost is...
Forum: Oxford Nanopore 01-10-2017, 08:35 PM
Replies: 2
Views: 1,393
Posted By ymc
Interesting. So the idea is to use your data and...

Interesting. So the idea is to use your data and submit paper to the conference?
Forum: Pacific Biosciences 01-10-2017, 12:24 AM
Replies: 2
Views: 1,069
Posted By ymc
Sounds good. Base accuracy seems to be...

Sounds good.

Base accuracy seems to be improved also. Any numbers?
Forum: Illumina/Solexa 10-31-2016, 06:08 AM
Replies: 2
Views: 541
Posted By ymc
What is Illumina Genome Network?

Does that mean it is the end for most service providers except for the niche ones? :confused:

https://grcf.jhmi.edu/dna-services/sequencing/whole-genome-sequencing/

"Whole Genome Sequencing
...
Forum: Oxford Nanopore 10-16-2016, 06:55 PM
Replies: 5
Views: 1,999
Posted By ymc
I think you can download Loman et al's E coli K12...

I think you can download Loman et al's E coli K12 MG1655 data. Supposedly all the reads should come from this genome. So you align the called fastq to the reference and see how well different mapper...
Forum: Illumina/Solexa 07-21-2016, 01:02 AM
Replies: 23
Views: 19,878
Posted By ymc
Suppose I can the sequence of the full 16S gene...

Suppose I can the sequence of the full 16S gene at high accuracy, which region(s) can give me the closest discriminating power to the whole gene sequence?
Forum: Oxford Nanopore 06-20-2016, 12:47 AM
Replies: 1
Views: 1,519
Posted By ymc
174GB E coli R9 data is also availabe:...

174GB E coli R9 data is also availabe: (Presumably from Nick Loman's team?)

https://t.co/Ljtl479fo9
Forum: Oxford Nanopore 05-30-2016, 06:24 PM
Replies: 7
Views: 2,422
Posted By ymc
http://omicsomics.blogspot.hk/2016/05/london-calli...

http://omicsomics.blogspot.hk/2016/05/london-calling-notes-on-brownian.html

No more R7 now. This thread can now also go to the dustbin as well. ;)
Forum: Oxford Nanopore 05-20-2016, 01:50 AM
Replies: 4
Views: 1,307
Posted By ymc
Thank you very much for your reply. Thanks...

Thank you very much for your reply.

Thanks for telling me that due to the unidentifiable hairpin adapter such that the boundary between template strand and complement strand is not clear,...
Forum: Oxford Nanopore 05-17-2016, 06:55 PM
Replies: 4
Views: 1,307
Posted By ymc
Thank you very much for your reply. So what...

Thank you very much for your reply.

So what is the difference between 2D reads and 1D reads that have both template and complement events? Could it be the former both template and complement come...
Forum: Oxford Nanopore 05-16-2016, 02:02 AM
Replies: 1
Views: 1,081
Posted By ymc
Sorry to interject my question into your thread....

Sorry to interject my question into your thread. I think it is somewhat relevant, so I hope you don't mind.

Based on my analysis of nanopore fast5 I downloaded from ENA, I noticed there are two...
Forum: Oxford Nanopore 05-05-2016, 07:56 PM
Replies: 5
Views: 1,386
Posted By ymc
http://biorxiv.org/content/early/2015/05/20/019281...

http://biorxiv.org/content/early/2015/05/20/019281

This preprint claims they can generate reads over 100kb. Please let us know if you can make it work. Good luck!
Forum: Oxford Nanopore 05-03-2016, 12:37 AM
Replies: 4
Views: 1,307
Posted By ymc
Does 1D complement-only read exist?

When I use poreminion fragstats to classify fast5's, theoretically I could use the 4th and 5th field to classify reads into 1D template-only, 1D complement-only, normal 2D and full 2D. In reality,...
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