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  • Count Base Pairs?

    I am new to DNA sequencing and I want to know is there any scripts or tools to count base pairs of a particular sequences. I am working on illumina HiSeq 2000.

  • #2
    Why would you count base pairs? And what does this have to do with the HiSeq2000? What is your goal? What are you planning to do?

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    • #3
      Originally posted by sphil View Post
      Why would you count base pairs? And what does this have to do with the HiSeq2000? What is your goal? What are you planning to do?
      Actually, I am just a technical research assistant helping out a researcher for some works of him.(means doesn't know much about dna sequencing) He wants that statistics and I can't figure out how to calculate that. I know how to count no. of spots,sequences but stuck in base pairs.

      For example,The following run have summary information such as # of Spots and runs. I already trimmed the adaptor sequences and merged the short reads. He wants the statistics of each process.

      I use FastQC and other tools to evaluate the sequence data. However,it doesn't provide the function to count base pairs.

      Any idea?

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      • #4
        Fastx-quality-stats from the FASTX-toolkit may give what you need.

        $ fastx_quality_stats -h
        usage: fastx_quality_stats [-h] [-i INFILE] [-o OUTFILE]

        version 0.0.6 (C) 2008 by Assaf Gordon ([email protected])
        [-h] = This helpful help screen.
        [-i INFILE] = FASTA/Q input file. default is STDIN.
        If FASTA file is given, only nucleotides
        distribution is calculated (there's no quality info).
        [-o OUTFILE] = TEXT output file. default is STDOUT.

        The output TEXT file will have the following fields (one row per column):
        column = column number (1 to 36 for a 36-cycles read solexa file)
        count = number of bases found in this column.
        min = Lowest quality score value found in this column.
        max = Highest quality score value found in this column.
        sum = Sum of quality score values for this column.
        mean = Mean quality score value for this column.
        Q1 = 1st quartile quality score.
        med = Median quality score.
        Q3 = 3rd quartile quality score.
        IQR = Inter-Quartile range (Q3-Q1).
        lW = 'Left-Whisker' value (for boxplotting).
        rW = 'Right-Whisker' value (for boxplotting).
        A_Count = Count of 'A' nucleotides found in this column.
        C_Count = Count of 'C' nucleotides found in this column.
        G_Count = Count of 'G' nucleotides found in this column.
        T_Count = Count of 'T' nucleotides found in this column.
        N_Count = Count of 'N' nucleotides found in this column.
        max-count = max. number of bases (in all cycles)

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        • #5
          Originally posted by GenoMax View Post
          Fastx-quality-stats from the FASTX-toolkit may give what you need.
          Thanks! GenoMax....that's a big help.

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