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  • anusha
    Junior Member
    • Jan 2010
    • 6
    #1

    Trimming or filtering the data from Solid

    Hi ..

    I have got the solid csfatsa file and the data has lot of dots in the sample. So i there any way i can trim or filter the Data in Bowtie,Maq or in another tools that you could suggest.
    Here the sample of the data.

    >1_17_228_F3
    T.1002.312..0..001.0001.2....1..1..022..0....00...0
    >1_17_469_F3
    T.1300.333..0..020.1020.0....0..1..020..3....01...3
    >1_17_578_F3
    T.1002.321..0..021.0230.0....1..2..122..1....11...2
    >1_17_581_F3
    T.1002.322..0..021.0011.0....2..1..021..2....20...1
    >1_112_1012_F3
    T.0300.3330.110021010300000000022130200.31.1.01.0.3
    >1_112_1459_F3
    T.1002.3201.002000003212002001021200223.10.3.30.2.3
    >1_113_39_F3
    T.1000.3330.000001000010100000121000220.10.0.01.0.0
    >1_113_233_F3
    T.1001.3211.012000000110102021021120220.00.0.31.2.0
    >1_113_329_F3
    T.1300.3330.011220010200000000122130200.01.0.01.0.3
    >1_113_835_F3
    T.1300.3330.012220010200002022122230202.01.1.01.2.3

    Thanks
    Anu
    Tags: None
    • nilshomer
      Nils Homer
      • Nov 2008
      • 1283
      #2
      Originally posted by anusha View Post
      Hi ..

      I have got the solid csfatsa file and the data has lot of dots in the sample. So i there any way i can trim or filter the Data in Bowtie,Maq or in another tools that you could suggest.
      Here the sample of the data.

      >1_17_228_F3
      T.1002.312..0..001.0001.2....1..1..022..0....00...0
      >1_17_469_F3
      T.1300.333..0..020.1020.0....0..1..020..3....01...3
      >1_17_578_F3
      T.1002.321..0..021.0230.0....1..2..122..1....11...2
      >1_17_581_F3
      T.1002.322..0..021.0011.0....2..1..021..2....20...1
      >1_112_1012_F3
      T.0300.3330.110021010300000000022130200.31.1.01.0.3
      >1_112_1459_F3
      T.1002.3201.002000003212002001021200223.10.3.30.2.3
      >1_113_39_F3
      T.1000.3330.000001000010100000121000220.10.0.01.0.0
      >1_113_233_F3
      T.1001.3211.012000000110102021021120220.00.0.31.2.0
      >1_113_329_F3
      T.1300.3330.011220010200000000122130200.01.0.01.0.3
      >1_113_835_F3
      T.1300.3330.012220010200002022122230202.01.1.01.2.3

      Thanks
      Anu
      Duplicate thread of:
      Trimming or filtering the data from Solid - SEQanswers
      http://seqanswers.com/forums/showthread.php?p=12759
      Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

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