Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • #46
    Oh well, I figured it out.

    I used ERX593921 data to polish the sample data which is from ERX708228 to ERX708231. After I used the fast5 from the correct archive, I was able to complete the run: (REF=polished, QRY=K12_MG1655)

    [REF] [QRY]
    [Sequences]
    TotalSeqs 1 1
    AlignedSeqs 1(100.00%) 1(100.00%)
    UnalignedSeqs 0(0.00%) 0(0.00%)

    [Bases]
    TotalBases 4614015 4641652
    AlignedBases 4612566(99.97%) 4620207(99.54%)
    UnalignedBases 1449(0.03%) 21445(0.46%)

    [Alignments]
    1-to-1 86 86
    TotalLength 4613201 4627972
    AvgLength 53641.87 53813.63
    AvgIdentity 99.23 99.23

    I think better error messages in this case will be welcomed.

    Comment


    • #47
      The ERX708228-31 data seems to have much higher yield for 2D reads than ERX593921. Why is that? Don't they all have the same R7.3 Chemistry? Or some sort of filter was applied for ERX708228-31? If so, what was that filter?

      Archive #read length #2Dread length 2Dyield
      593921 70531 311.56M 11823 64.53M 20.71%
      708228 25353 150.33M 8451 52.26M 34.76%
      708229 16917 61.57M 5639 21.91M 35.58%
      708230 8565 46.05M 2855 16M 34.74%
      708231 15975 123.29M 5325 43.44M 35.24%

      Comment


      • #48
        I read the two papers more carefully and noted the versions of Chemistry, Sequencing Kit and Metrichor for each run:

        ERX593921 is (R7.3, SQK-MAP-003, Metrichor 1.2.2 r1.5)
        ERX708228 is (R7.3, SQK-MAP-003, Metrichor 1.9)
        ERX708229-31 is (R7.3, SQK-MAP-003, Metrichor 1.9)

        So the difference was due to using older version of Metrichor for ERX593921?

        Does each run correspond to one ONT box? If that's the case we are only getting 133.6Mb for $4,000? Then ONT is not competitive at all in bacterial de novo assembly, right?

        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
        11 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        51 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        68 views
        0 likes
        Last Post seqadmin  
        Working...
        X