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  • Need help reading this data

    Hi I am a computer science graduate student and need help reading some data for this bioinformatics research I am helping out on. I have a few hundred text files containing the following sample information:

    Geno SNP_A-8343733 NA
    Geno SNP_A-8338245 1
    Geno SNP_A-8338251 NA
    Geno SNP_A-8338258 0
    Geno SNP_A-8344803 1
    Geno SNP_A-8349310 1

    I want to know how to read this data and what kind of data is this? I am new to Biology and Bioinformatics in general so any help would be greatly appreciated!

  • #2
    check out "affymetrix array snp calling" output formats and codes

    SNP_A* are snp ids (which map to dbSNPS's rsIDS)

    The code is probably ...
    0=AA (homozygous for the reference allele)
    1=AB (heterozybous)
    2=BB (homozygous for the alternative allele)

    but make sure.

    Comment


    • #3
      Okay thank you. I found out that it is affymetrix array snp calling 6.0 but not sure what I can do with this data exactly?

      Comment

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