Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • #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

    Comment


    • #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).

      Comment


      • #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.

        Comment


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



          Last edited by GenoMax; 12-20-2014, 02:07 PM.

          Comment


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



            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.

            Comment


            • #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=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”.

              Comment

              Latest Articles

              Collapse

              • seqadmin
                Strategies for Sequencing Challenging Samples
                by seqadmin


                Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                03-22-2024, 06:39 AM
              • seqadmin
                Techniques and Challenges in Conservation Genomics
                by seqadmin



                The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                Avian Conservation
                Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                03-08-2024, 10:41 AM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, Yesterday, 06:37 PM
              0 responses
              11 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, Yesterday, 06:07 PM
              0 responses
              10 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-22-2024, 10:03 AM
              0 responses
              51 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-21-2024, 07:32 AM
              0 responses
              68 views
              0 likes
              Last Post seqadmin  
              Working...
              X