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  • fasta sequence: 0 based or 1 based index

    When we say the position of a sequence, is zero based or one based?
    Because I want to extract a sub sequence from a long one.
    Code:
    AGCTTT
    012345
    OR
    Code:
    AGCTTT
    123456
    Thanks.

  • #2
    That is undefined if you don't specify which system (or language) you're working with.

    Comment


    • #3
      Okay. If the sequence is given and a position 63150935 is given as well. I want to get 1000kb size around this point by C#.
      Then
      Code:
      string trunk = sequence.Substring(63150935-500000,1000000);
      or
      Code:
      string trunk = sequence.Substring(63150934-500000,1000000);
      Which one is correct?
      Last edited by ardmore; 11-15-2011, 08:26 AM.

      Comment


      • #4
        In c# the indices are 0 based, so the first one would be apppropriate if your position is also defined as 0 based.

        If it was 1 based (for example, if it comes from Ensembl), you'll need to do the second one though.

        Comment


        • #5
          My question is not for C#. I meant that I am not sure whether the sequence is defined as 0 based or not. The sequence is a fasta file or extracted from a genome.

          Comment


          • #6
            The sequence is not your issue. A sequence itself is not '0 based', it's just a list of characters.
            Where does your position 63150935 come from?

            Comment


            • #7
              It is from a bam file output. If we define a region such as chr22:10000-20000.
              And we get the consensus sequence, we only interest one small region around a specific position.
              How to?

              Comment


              • #8
                If it's from a BAM/SAM file, then look at the BAM/SAM specification:

                http://samtools.sourceforge.net/SAM1.pdf

                For example, the fourth field of SAM files is 1-based:
                POS: 1-based leftmost mapping POSition of the first matching base. The first base in a reference
                sequence has coordinate 1. POS is set as 0 for an unmapped read without coordinate. If POS is
                0, no assumptions can be made about RNAME and CIGAR.
                whereas the internal BAM representation is 0-based:
                pos / 0-based leftmost coordinate (= POS − 1) / int32 t / [-1]

                Comment


                • #9
                  Thank you.

                  Comment

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