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  • 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.

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