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  • Coordinating sequencing data and microarrays

    I'm sure this is a very simple question, but I am still getting a feel for how locations are named.

    Let's assume that I've processed an individual's genome (possibly from 1000 genomes) and I identified a consensus sequence for that individual.

    I want to compare the sequencing calls to microarray calls for those SNPs on an array. How do I identify the positions in the sequencing that are located on the array?

  • #2
    Originally posted by bio View Post
    I'm sure this is a very simple question, but I am still getting a feel for how locations are named.

    Let's assume that I've processed an individual's genome (possibly from 1000 genomes) and I identified a consensus sequence for that individual.

    I want to compare the sequencing calls to microarray calls for those SNPs on an array. How do I identify the positions in the sequencing that are located on the array?
    This seems like an extremely basic bioinformatics question. I would ask your local bioinformatician or your PI for help getting accustomed to such data.

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    • #3
      1000 Genomes microarray data

      In the specific instance of 1000 Genomes data, does anyone know if the microarray calls or (preferably) raw array data are available for download? These were used to validate NSG-based SNP calls as mentioned in the pilot paper. Further, for full project data (e.g. high coverage full exome), will this data be made available as it is generated? Is some of it already available?

      I haven't seen this data at the project FTP site.

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