Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • a conflict in newbler graph file

    Hi All,

    I have following information in newbler graph file. it looks like flow and pairend infor of contig1600 are not correct. it has a conflict with other information. 1600 edge info shows 1600 connects to 178997 at 3'. but 1600 flow infor shows it connects to 178997 at 5'. and from the neighbor's infor, I think 1600 and 1601 should switch each other. Do I misunderstand something? or newbler has a bug?

    Thanks
    xu


    C 1599 3' 1601 5' 6
    C 1599 3' 729451 3' 8
    F 1599 - 729451/8/0.0;1601/6/0.0;948623/3/300.0
    P 1599 1598/6/835.3;237643/3/2453.0 1601/3/471.7;240469/2/757.5;1602/2/3584.0

    C 1600 3' 178997 5' 14
    F 1600 178997/14/0.0 1009123/7/0.0;729451/3/150.3
    P 1600 1602/5/2002.0;1604/4/5496.5 1601/5/719.4;1597/3/5458.3

    F 1601 1599/6/0.0 -
    P 1601 1599/3/471.7;1598/5/1492.4;1596/6/5305.2 1600/5/719.4;178997/6/1558.7;1602/2/3534.5

    C 1602 5' 286407 5' 11
    F 1602 289179/8/0.0;286407/11/0.0 -
    P 1602 289179/2/81.5;286407/5/106.2;178997/14/779.4;568843/2/1369.0;240469/5/1579.4;1600/5/2002.0;507748/2/2265.0;1601/2/3534.5;1599/2/3584.0;907492/2/4066.0;1598/6/4098.8 1604/5/0.0;1603/9/253.3;192075/3/2199.3;1605/5/3330.4;389573/2/3431.0;254877/3/3613.3

    F 178997 240469/13/0.0;1600/14/0.0 289179/9/0.0;286407/4/0.0
    P 178997 1601/6/1558.7;1026832/2/1960.0;1598/5/3231.8 1602/14/779.4;192075/3/5457.3

    C 1009123 5' 1600 5' 7
    F 1009123 1180328/12/0.0;1600/7/0.0;240469/11/48.0 729451/8/0.0
    P 1009123 240469/2/2193.0 -

    so I think the correct 1600 info should be:
    C 1600 3' 178997 5' 14
    F 1600 1009123/7/0.0;729451/3/150.3 178997/14/0.0
    P 1600 1601/5/719.4;1597/3/5458.3 1602/5/2002.0;1604/4/5496.5
    Last edited by zxybl; 10-17-2012, 11:05 AM.

  • #2
    It does indeed look strange. You may want to contact 454 about this...

    Comment


    • #3
      there is a bug in this version. and it has been fixed in new v2.8.

      Comment


      • #4
        Ah, good to know. Which version contains the bug?

        Comment


        • #5
          it is a beta version and not released for public.
          Last edited by zxybl; 10-23-2012, 06:57 AM.

          Comment

          Latest Articles

          Collapse

          • seqadmin
            The Impact of AI in Genomic Medicine
            by seqadmin



            Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
            Yesterday, 02:07 PM
          • seqadmin
            Multiomics Techniques Advancing Disease Research
            by seqadmin


            New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

            A major leap in the field has
            ...
            02-08-2024, 06:33 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 02-23-2024, 04:11 PM
          0 responses
          44 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-21-2024, 08:52 AM
          0 responses
          60 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-20-2024, 08:57 AM
          0 responses
          49 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-14-2024, 09:19 AM
          0 responses
          65 views
          0 likes
          Last Post seqadmin  
          Working...
          X