Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • CNVnator: The format of cnv result

    I know CNVnator has been used in 1000 Genomes Project. But there is little of material to explain the format of CNV result. Is there anyone know the format of cnv result? For example:
    deletion chr10:6070441-6074520 4080 0.674906 0.00834134 72162.3
    It is very easy to understand the first three column mean, but is there any can explain the rest of column mean?

  • #2
    This is what I got from the author of CNVnator:

    CNV_type coordinates CNV_size normalized_RD p-val1 p-val2

    normalized_RD -- normalized to 1.
    p-val1 -- is calculated using t-test statistics.
    p-val2 -- is from probability of RD values within the region to be in
    the tails of gaussian distribution describing frequencies of RD values in bins.

    Comment


    • #3
      Thx bioworker,
      I think it will help me a lot.

      Comment


      • #4
        Do the graphs make any sense? It would be great if any of you can explain it to me.

        I graphed the below region and here is what I get:
        Code:
        duplication chr1:172376901-172381900	5000	10.2	2.54996e-10	2.65008e-29

        Comment


        • #5
          So is there any rules should be used to filter the results based on p-val1 or p-val2? Or all the output on screen are candicate?

          Comment


          • #6
            same question: how to filter result, and which p-val should be considered?

            Comment


            • #7
              same doubt - how to filter the CNVs.
              Maybe p-value of <0.01 or <0.05
              And about the size of CNVs?

              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