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  • How to create .fastq file?

    Hi everybody,

    I'm new member and I'm new to Bioinformatics too.
    I'm using bwa. 0.6.2. I've chr1.fa reference genome file.
    I don't know how to create the .fastq file corresponding to my
    reference file. Do you have any idea?

    Many thanks,
    Best,

    nazo
    Last edited by sinopnazo; 02-01-2013, 04:39 AM.

  • #2
    What sequencing platform are you using? What is the format of your sequencing data?

    Comment


    • #3
      I couldn't understand the question, but I'm using human genome (hg19) and I downloaded chromFa.tar.gz file.
      I indexed human choromosome 1 in bwa, but I don't know how to align my fastq file to it. Because I couldn't create its fastq file.

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      • #4
        Your sequencing data is the fastq file.

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        • #5
          Then I expressed myself completely wrong. I don't have sequencing data, I'm trying to have one. I only have chr1.fa.

          Comment


          • #6
            Try the ENA at EBI or the SRA at NCBI.

            Comment


            • #7
              Right, let's start at the very beggining. I see that you have done a little bit of reading on the topic and I understand that it might be confusing. Firstly, I assume that you are trying to answer a specific question using bioinformatics. What is your question, what exactly do you want to investigate? The more information you include the more likely people here will be to help you. Secondly, FASTQ is a format that stores your sequence and its quality score. Read the wiki page, link above. It is possible to download publicly available sequences from e.g. for human http://www.ncbi.nlm.nih.gov/Traces/s...obj&term=human They use .sra format, which you will have to convert to FASTQ using sra toolkit. Explanation - http://www.ncbi.nlm.nih.gov/books/NBK56562/ However, I would advise against downloading any of these sequences until you know exactly what you are trying to do. http://www.csc.fi/english/csc/course...e/ngs_workshop - this is a good resource for some basic information. If you find it too difficult, you can start with this workshop http://www.bioinf.uni-leipzig.de/~da...p_evop2012.pdf and wikipedia.

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              • #8
                Thank you so much.

                It seems a lot of things to do...
                I'll try sra toolkit.

                Best,
                nazo.

                Comment

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