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  • SOAP and quality

    I am using SOAP to map my reads on the human genome.
    Since SOAP can work with .fasta or .fastq files, I thought it checks the quality when running.
    But I have the exact same results with my .fasta and my .fastq file, so I wonder if SOAP really cares about quality?

  • #2
    Originally posted by Insane View Post
    I am using SOAP to map my reads on the human genome.
    Since SOAP can work with .fasta or .fastq files, I thought it checks the quality when running.
    But I have the exact same results with my .fasta and my .fastq file, so I wonder if SOAP really cares about quality?
    I don't think it makes a difference in the alignment at all. But when assessing bases that differ from the reference, it helps to know if the differing base is of high quality or not.

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    • #3
      Originally posted by Insane View Post
      I am using SOAP to map my reads on the human genome.
      Since SOAP can work with .fasta or .fastq files, I thought it checks the quality when running.
      But I have the exact same results with my .fasta and my .fastq file, so I wonder if SOAP really cares about quality?
      Are you referring to SOAP2 or SOAP v.1?

      If v.1, then my impression was that it doesn't really deal with quality, only keeps it aligned to the sequences at the time of the report. Which is convenient.

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      • #4
        Thank you for your answers.
        I was refering to SOAP2 but maybe there is no difference between the 2 versions for this criteria...

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