Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • MUMmer plot full of dots and no diagonal lines

    I know from the MUMmer manual that a perfect alignment should, ideally, show a red diagonal line going from the bottom to up in the plot. However, I used MUMmer plots to compare the results of the assemblies between Velvet and Minia (both assemblies performed using the same kmer size and same coverage cutoff). And I received the following plot, I am wondering whether this is good alignment or a terrible one?


  • #2
    If these are two related species, its a terrible alignment.

    Which search algorithm did you use? It makes a big difference:
    • mummer, efficiently locates maximal unique matches between two sequences
    • NUCmer (NUCleotide MUMmer), for closely related sequences
    • PROmer (PROtein MUMmer), using six frame translation of DNA input, for less similar sequences

    Comment


    • #3
      You say "...results of the assemblies between Velvet and Minia ". How are the assemblies sorted? If they are not in the same order then the alignment will look random.

      Comment


      • #4
        Actually back-tracking slightly, looking more closely at the vertical axis, all the contigs are so small that you won't see any diagonal lines in the mummer plot. The horizontal scale has some nice long contigs.

        There is probably a mummer option to sort the contigs, in which case you'd hope to get dots on a diagonal...

        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
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        9 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
        67 views
        0 likes
        Last Post seqadmin  
        Working...
        X