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  • Convert FASTA to FASTAQ

    Hi

    I need to map small RNA sequences onto a genome using BWA.

    The read file (reads.fa) is in the following format:

    >EMUNAOL01D19UY length 23 duplications 0
    CGTCTTGGTTTGTCTAAAGGGGC
    >EMUNAOL01EK9BY length 24 duplications 0
    TGGTGGAGGCCCGCAGCGATACTG
    >EMUNAOL02GZHTT length 24 duplications 0
    GGGCAAAAGTACAAAGTTCATGTG
    >EMUNAOL02IQUC1 length 24 duplications 0
    AGAAATGTTGCTACATAAATTGGA

    How can I convert this file to a FASTAQ file (reads.fastq) suitable for BWA?

    I tried maq but I couldn't get it to work - it just produced a file of 0 bytes - so i'm not sure if it's suitable for what i'm trying to do. Is there another program might be useful?

    Thanks

    Jon
    Last edited by jomaco; 10-30-2011, 06:15 AM.

  • #2
    BWA accepts reads in the fasta format.

    Comment


    • #3
      Sorry. You're right it does. Someone who asked me to run the alignment told me it was required to convert the read file to fastaq format. Perhaps I should not be so trustful next time!

      I have now managed to get the alignment to run. Thanks for your reply

      Comment


      • #4
        What's this "FASTAQ" format? Do you mean "FASTQ"?

        Comment


        • #5
          I believe "FASTAQ" is a typo, but actually fasta+fastq is really a fastaq format. You can mix fasta and fastq records in one file with no problem. A multi-line fastq parser can be trivially modified to parse such a file. This is basically what my fastq/fasta parser is doing. To most of my recent programs (maq excluded), fasta and fastq are the same format.

          Comment


          • #6
            Mixing FASTA and FASTQ into one file... that strikes me as a strange and dangerous idea, although I can see uses for it (combining raw read datasets of different types into one file for alignment).

            Comment


            • #7
              I am not saying this is a good format. I am saying that there should really be one parser instead of two.

              Comment

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