Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Significance of Overlapping Regions

    I have two bed files of genomic coordinates. (say 12000 entries in one, 1000 in the other) I know how many unique bases in the genome are covered by each file (say 12000=15% of the genome, 1000=3% of the genome. I overlap them and get a result, say 50% of the 1000 overlap the entries in the 12000. Does anyone have suggestions on how to test the significance of this given that any overlap (not complete) is counted as overlap? I've thought of adding expanding the refernence (12000) entries by 50% of the average length of the 1000 entries, but that seems a bit to crude.

  • #2
    You can do a Monte carlo against randomly distributed regions, or even regions randomly distributed that are still the same distance to TSS or such. Will basically always call your result significant though, because the null model is bad.

    Comment


    • #3
      Sorry what does your last sentence mean? My plan is to use shuffleBed with intersectbed over 1000x and then plot the distribution of intersections and see where the actual data falls on the plot. Is that not sound?

      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