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  • kwtennis311
    replied
    thanks

    thanks guys, Biopython did the trick

    Leave a comment:


  • Bio.X2Y
    replied
    Thanks sklages! I wasn't aware of qual files.

    kwtennis311, there seem to be some existing posts on this, you might find answers in this, e.g. http://seqanswers.com/forums/showthread.php?t=3730.

    Leave a comment:


  • sklages
    replied
    Originally posted by Bio.X2Y View Post
    However, I don't think it makes any sense to create a fasta file "containing the quality scores". Fasta files are used to represent sequences.
    ... and their corresponding qualities ..

    mySeq.fasta :
    >mySeq
    ACGTACGT

    mySeq.fasta.qual:
    >mySeq
    22 22 33 33 22 22 33 44

    There are still some programs which need to be fed with fasta/qual :-)

    Anyway, qualities need to be converted to phred-stye ..

    Leave a comment:


  • Bio.X2Y
    replied
    You could use awk to create a simple fasta file from your fastq, e.g.

    awk 'NR % 4 == 1 {print ">" $0 } NR % 4 == 2 {print $0}' my.fastq > my.fasta

    However, I don't think it makes any sense to create a fasta file "containing the quality scores". Fasta files are used to represent sequences.

    Leave a comment:


  • kwtennis311
    started a topic fastq to fasta conversion

    fastq to fasta conversion

    How can I convert my fastq files to two fasta files with one containing the reads and another containing the quality scores?

    Thanks

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