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  • Fastq to Fasta

    Hello I want to convert fastq to fasta, by google search I got a perl code.
    http://edwards.sdsu.edu/labsite/inde...fasta-and-qual
    However my perl knowledge is almost zero, I don't know how to run this script. Do I need to input arguments for input or output file?
    Please give me an example.


    Thanks.

  • #2
    use awk :
    awk 'BEGIN{P=1}{if(P==1||P==2){gsub(/^[@]/,">");print}; if(P==4)P=0; P++}' input.fastq > output.fasta

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    • #3
      Ardmore, you are cluttering the forum with questions that can be resolved by looking at existing, easily located resources on the Internet. I've previously voiced my concerns in another thread that you are trying to use the forum to solve coursework problems which in my opinion is not a legitimate use for it.

      My feeling is there's only so much time and effort the community should be prepared to put into newbie questions like yours. I would suggest you enrol in a basic course on scripting and/or bioinformatics, read some basic bioinformatics tutorials, or find a mentor at your institution who can help you.

      If you feel I am being unfair, perhaps you can explain what your project is and why we should help you with basics like running perl scripts.

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      • #4
        I understand your concern. But I am not a student for my course worker. Actually my major is not bioinformatics but I am doing daily bioinformatics project. Maybe I selected a wrong career? I don't have a time to enroll a perl course because the work is due very soon and perl is rarely used.

        I hope this forum can have a subforum for newbie. Thanks for your time and advice. I will keep quite in this forum.

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        • #5
          It's not that you are a newbie. This field is only a few years old, everyone here started as a newbie just a few years ago. But everyone else started by reading some documentation, so that they understood what the hell they were talking about. You don't even know what a fastq file is!

          By posting here, you are asking people to spend their own time to answer your questions. People are by and large willing to do that, but not when you have demonstrated that you haven't invested a lick of your own time to understand even the basics of the work you are trying to do.

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          • #6
            I like the awk script. I modified a perl snip I found to also convert '.' to 'N' I found in some Illumina fastqs:

            cat FILEIN | perl -e '$i=0;while(<>){if(/^\@/&&$i==0){s/^\@/\>/;print;}elsif($i==1){s/\./N/g;print;$i=-3}$i++;}' > FILEOUT

            Just change filein and fileout as appropriate.
            Good luck.

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            • #7
              Also try the fastx toolkit.

              http://hannonlab.cshl.edu/fastx_tool...to_fasta_usage

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