Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • #16
    Originally posted by huguesparri View Post
    At the moment, 150pb read are not supported by Illumina on the Hiseq2000.
    I think it's still possible to run it on the machine but there is a strong probability that your error rate explode at the end of the read. And I don't think it will be suitable for your application.
    Unofficially, our FSE told us that a "correct" error rate for a 100nt read was below 2% (I think it was V2 kits a that time, it may have vary with V3 kits). I won't be surprise if your reach 4 to 5% error rate with a 150nt read.
    Here is a plot of the error rate (phiX) for our most recent HiSeq2000 run:



    Just for the top surface. Bubbles drive the error rate up higher for the bottom surface. Even so the error rate at 100 bases is generally below 0.5%.

    The Sequence Analysis Viewer (SAV) shows >80% of the reads with no errors (counting both surfaces). Again, this is based on aligning phiX reads spiked into 7 lanes of the flowcell to phiX by the instrument software.

    --
    Phillip

    Comment


    • #17
      I've checked our last 2*100nt run. On the PhiX control lane, error rate is between 0.8 and 1%. But for the spiked PhiX in our sample, it's just above 1%.
      :'(

      Comment


      • #18
        MiSeq is now capable of 2x250b PE

        Comment


        • #19
          Also the upgraded MiSeq gives 16 million reads.

          Comment


          • #20
            Originally posted by NextGenSeq View Post
            Also the upgraded MiSeq gives 16 million reads.
            16million clusters or reads?

            Comment


            • #21
              Reads....there are many more clusters... Without the upgrade MiSeq produces up to 5 million reads.

              Comment


              • #22
                Originally posted by JackieBadger View Post
                Reads....there are many more clusters... Without the upgrade MiSeq produces up to 5 million reads.
                No, with the upgrade the output is 15-17 million CLUSTERS. This makes 30-34 million PE reads.

                Comment


                • #23
                  What exactly is it that limits the read length anyways?
                  I understand imperfect cleavage of fluorescence reduces the # of extending oligos, lowering the signal + adding noise.
                  Also, eventually some oligos get "out of phase" and then muddy the signal. Is this somewhat caused by insufficient purging of reagents from previous cycles?

                  Thanks.
                  Jim

                  Comment

                  Latest Articles

                  Collapse

                  • seqadmin
                    Strategies for Sequencing Challenging Samples
                    by seqadmin


                    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                    03-22-2024, 06:39 AM
                  • seqadmin
                    Techniques and Challenges in Conservation Genomics
                    by seqadmin



                    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                    Avian Conservation
                    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                    03-08-2024, 10:41 AM

                  ad_right_rmr

                  Collapse

                  News

                  Collapse

                  Topics Statistics Last Post
                  Started by seqadmin, Yesterday, 06:37 PM
                  0 responses
                  8 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, Yesterday, 06:07 PM
                  0 responses
                  8 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 03-22-2024, 10:03 AM
                  0 responses
                  49 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 03-21-2024, 07:32 AM
                  0 responses
                  66 views
                  0 likes
                  Last Post seqadmin  
                  Working...
                  X