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  • #16
    I only vaguely remember the details of the project from your deleted post, but if I were to guess what a reasonable assignment would be, it would be to select a cancer gene, then extract 1 Mb of sequence around the gene from ten different individual genomes, then analyze those 1 Mb regions for the various things asked for in the post.

    You aren't going to find 1 Mb fastq reads, but you can find different individual genomes, or even different "cancer" genomes. You can definitely identify genes related to cancer. As others have said, I'd check back with the assigner of this project for clarification.

    edit: I teach an upper level course in genomic methods and analysis, so am definitely curious what this assignment is about!
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

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    • #17
      I like SNPsaurus' interpretation. 1 Mb (total amount of data or length of region covered) worth of fastq reads in and/or around a cancer gene makes sense.

      @SNPsaurus: Main input for the assignment is still in post #6. The rest of the assignment was informatics goals.

      This will entail a significant amount of work (data collection part) and I hope the assignment has an appropriate amount of credit (unless it is a PhD qualifier exam).

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      • #18
        Alright... Let's say my oncogene of interest is in the region of 11:15000000..16000000. Therefore, all I need is that region from 10 different people.

        Problem:
        Where do I find that data???

        Any assistance is appreciated.

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        • #19
          Look for studies that have > 10 samples (since you need 10) or take 10 samples from different cancer types.

          http://sra.dnanexus.com/?result_type...q=tumor+exome+

          http://sra.dnanexus.com/?result_type...q=cancer+exome
          Last edited by GenoMax; 12-20-2014, 02:07 PM.

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          • #20
            The comments here have links to sequences for PUBLIC human cancers ...

            http://www.homolog.us/blogs/blog/201...able-from-bgi/

            BGI liver cancer
            Seoul Genomic Medicine Institute lung cancer
            Changhai Hospital prostate cancer
            MD Andersen Asian Gastric cancer

            I think the data is in NCBI's SRA

            You'll need a lot of disk space and, if you're relatively new, a lot of patience.

            Sadly, a "bam slicer" that cuts out the reads for a region isn't available; though they say some folks are working on it.

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            • #21
              Originally posted by GenoMax View Post
              Look for studies that have > 10 samples (since you need 10) or take 10 samples from different cancer types.

              http://sra.dnanexus.com/?result_type...q=tumor+exome+

              http://sra.dnanexus.com/?result_type...q=cancer+exome
              Thank you. I think I want to get the same region from 10 different people.

              Access an online cancer related DNA database resource and select ten (10) DNA sequence strings of length at least 1Mb related to a cancer gene from ten different individuals. Make sure the sequence data is in FASTQ format and stored in one file “DNA.fas”.

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              • #22
                You aren't going to find 1 Mb fastq reads, but you can find different individual genomes gas-stationsnearme.com or even different "cancer" genomes. You can definitely identify genes related to cancer. As others have said, I'd check back with the assigner of this project for clarification.

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                • #23
                  You are not going to find DNA sequences in fastq format that are 1Mb in length unless you assemble them yourself preserving the Q-scores (assembly programs do not include Q-scores in final sequence).

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