Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • AllSeq
    replied
    Originally posted by nucacidhunter View Post
    With all discussions in this thread I wondering if there will be any issue if I spike-in 500 ng of non-human DNA in 0.0001 pg of human DNA sample and submit it for sequencing on a HiSeq X Ten. The obvious reason is cheaper sequencing of non-human spike-in DNA.
    Now you don't need to! Illumina just opened up the HiSeq X to run non-human samples: http://www.businesswire.com/news/hom...e#.VhQNtdZPRuI

    But it still only runs WGS. Any bets on when the application menu opens up?

    Leave a comment:


  • jwfoley
    replied
    I think when you invest ten million dollars in machines that can only be used with consumables from one company, you don't take unnecessary risks that might be construed as a breach of contract.

    Leave a comment:


  • AllSeq
    replied
    Originally posted by nucacidhunter View Post
    With all discussions in this thread I wondering if there will be any issue if I spike-in 500 ng of non-human DNA in 0.0001 pg of human DNA sample and submit it for sequencing on a HiSeq X Ten. The obvious reason is cheaper sequencing of non-human spike-in DNA.
    You can do that, but the built in informatics will choke (it's expecting human DNA) and you'll be violating the agreement that the X Ten owner signed when they bought it. It probably won't take Illumina too much effort to figure out what's going on.

    Leave a comment:


  • nucacidhunter
    replied
    With all discussions in this thread I wondering if there will be any issue if I spike-in 500 ng of non-human DNA in 0.0001 pg of human DNA sample and submit it for sequencing on a HiSeq X Ten. The obvious reason is cheaper sequencing of non-human spike-in DNA.
    Last edited by nucacidhunter; 05-16-2014, 04:27 PM.

    Leave a comment:


  • TonyBrooks
    replied
    Originally posted by jwfoley View Post
    Are you tied to Basespace for data management, or is there a way to copy to a networked drive (either as the run is being performed or after the run has finished)? I'd like to understand a little bit more about how the data is moved around.
    You have the option of specifying a network location to mirror the run and send it up to BaseSpace for run monitoring. You can then use the new version of bcl2fastq to demultiplex and make fastq. There is no fastq only option for BaseSpace, you need to run it through a pipeline to make fastq and just ignore the results of the analysis.

    Leave a comment:


  • jwfoley
    replied
    Also what kind of connectivity does the thing have besides networking? Since it's targeted at mid-level labs and not large facilities, it won't always be in pipelines that immediately dump everything to a computing cluster, let alone BaseSpace. I just ran a month-old MiSeq yesterday that's not even networked (though we don't have gigabit ethernet so fat lot of good that would do anyway) and I had to copy out my data through a USB2.0 port - what year is this? So with NextSeq-scale data volumes, this matters.

    Leave a comment:


  • bilyl
    replied
    Originally posted by williamhorne View Post
    Using High output we are actually getting over 500 million reads per run. Unlike our GAII, and HighSeq, we actually have to pay very close attention to cluster density. The target cluster density for high quality samples is 1.75pM-2pM. Anything above and below will results in under/over clustering. So your samples need to be very exact with concentration.

    These are solely made to be streamlined with the BaseSpace. Right now it only works with BaseSpace onsite, not in the cloud as they are having some majority broker issues that still are not resolved. Make sure you do your research in regards to output files and data in regards to basespace because it is not a visual machine. It gives you the output files and you must use 3rd party software on a different computer to view the results. Very annoying.

    Overall very impressed with the NextSeq's, not so much BaseSapce.
    Are you tied to Basespace for data management, or is there a way to copy to a networked drive (either as the run is being performed or after the run has finished)? I'd like to understand a little bit more about how the data is moved around.

    Leave a comment:


  • williamhorne
    replied
    Using High output we are actually getting over 500 million reads per run. Unlike our GAII, and HighSeq, we actually have to pay very close attention to cluster density. The target cluster density for high quality samples is 1.75pM-2pM. Anything above and below will results in under/over clustering. So your samples need to be very exact with concentration.

    These are solely made to be streamlined with the BaseSpace. Right now it only works with BaseSpace onsite, not in the cloud as they are having some majority broker issues that still are not resolved. Make sure you do your research in regards to output files and data in regards to basespace because it is not a visual machine. It gives you the output files and you must use 3rd party software on a different computer to view the results. Very annoying.

    Overall very impressed with the NextSeq's, not so much BaseSapce.

    Leave a comment:


  • M4TTN
    replied
    Originally posted by williamhorne View Post
    I bought the first two NextSeq 500's and basespace onsite. So if anyone has any questions please feel free to email me.
    I'd be interested to know the costs of the various kits and the output you are getting (in cluster number).

    Leave a comment:


  • williamhorne
    replied
    I bought the first two NextSeq 500's and basespace onsite. So if anyone has any questions please feel free to email me.

    Leave a comment:


  • GW_OK
    replied
    Originally posted by pmiguel View Post
    My Illumina sales rep told me:
    Not sure how Illumina can enforce this, but the word is that it will.
    Usage license. A piece of paper is signed saying you will only ever run Human WGS on these sequencers.

    Leave a comment:


  • GenoMax
    replied
    Those who want/could use patterned flowcells need to start hoarding (thousands of) dollars. That way one will be ready when HiSeq X becomes available for purchase as a stand-alone instrument.

    In case you had missed this from yesterday: http://seqanswers.com/forums/showthread.php?t=40314
    Last edited by GenoMax; 01-28-2014, 03:12 PM.

    Leave a comment:


  • pmiguel
    replied
    My Illumina sales rep told me:

    (1) Patterned flowcells are only for the HiSeqX.
    (2) As previously reported only HiSeqs with certain serial numbers can run the v4 SBS chemistry. There is no upgrade path for HiSeqs outside that serial number range.
    (3) The HiSeq X Ten may only be used for sequencing human genomic DNA libraries constructed with TruSeq Nano DNA prep kits. Not sure how Illumina can enforce this, but the word is that it will.

    --
    Phillip

    Leave a comment:


  • austinso
    replied
    Originally posted by GenoMax View Post
    We are assuming that there will be a "patterned" flowcell kit for 2500. I found this blog post (skip to the "Edit" at the bottom of the post), which says that "patterned" flowcells will only work with HiSeq X and TruSeq Nano kits.

    Let us hope that is not true.
    Based on the flow-cell description for the HiSeqXTen, my guess is that significant mods would be required to allow 1. current to be linked the electrodes of the flow cell and 2. to control the current and the fluidics in a way to permit ordered cluster generation...

    FWIW

    Leave a comment:


  • pmiguel
    replied
    Originally posted by GenoMax View Post
    We are assuming that there will be a "patterned" flowcell kit for 2500. I found this blog post (skip to the "Edit" at the bottom of the post), which says that "patterned" flowcells will only work with HiSeq X and TruSeq Nano kits.

    Let us hope that is not true.
    The patterned flowcell may only work with the HiSeq X Ten, but I fail to see how a TruSeq Nano library molecule is distinguishable from any other (modern) Illumina library molecule.

    --
    Phillip

    Leave a comment:

Latest Articles

Collapse

  • seqadmin
    Genetic Variation in Immunogenetics and Antibody Diversity
    by seqadmin



    The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
    11-06-2024, 07:24 PM
  • seqadmin
    Choosing Between NGS and qPCR
    by seqadmin



    Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
    10-18-2024, 07:11 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 11-08-2024, 11:09 AM
0 responses
59 views
0 likes
Last Post seqadmin  
Started by seqadmin, 11-08-2024, 06:13 AM
0 responses
38 views
0 likes
Last Post seqadmin  
Started by seqadmin, 11-01-2024, 06:09 AM
0 responses
35 views
0 likes
Last Post seqadmin  
Started by seqadmin, 10-30-2024, 05:31 AM
0 responses
23 views
0 likes
Last Post seqadmin  
Working...
X