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  • phap/phred : using fastq quality

    Hi,

    Is there any way phrap uses fastq quality ?

    In manuals and over the internet no results found :s

    Thx for your help

  • #2
    What do you exactly mean? AFAIR phrap uses fasta/qual.

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    • #3
      I would like to use phrap with quality values.
      But the only quality i have is in fastq format.
      Phrap with fastq input file returns error as sequences don't begin with ">" (but "@"). Thus, how can I convert fastq files to be used by phrap (WITH quality)?

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      • #4
        AFAIR phrap only uses fasta/qual.

        Convert your fastq to fasta/qual with your tool of choice (e.g. convert_project from MIRA assembler package) and then feed phrap with the resulting fasta/quals.

        Have a look at http://phrap.org/phredphrap/phrap.html (3. Quality files.)
        The name of this file must consist of the name of the FASTA file, with ".qual" appended.
        The online docs are quite old but there is a README shipped with the Phrap software distribution which contains more up-to-date info.

        hth, Sven

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