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  • SNP array analysis

    I there!!
    A friend has passed me the data of an Infinium Omni5-4 array. In short, they have applied two different mutagens to a cell line. I have passed a data set that contains:
    3 mother samples (MS)
    3 samples mutagene 1 (M1)
    3 samples mutagene 2 (M2)
    Its objective is to identify the mutagenic potential of each mutagene.
    After googeling, I think what I need to do is a Manhattan plot to identify the chromosomal regions that have mutated the most for each mutagene.
    What I have done at the moment is:
    1 Genotyping callin, using the Genotyping Module of Genome Studio
    2 Establish the reference set: SNP's 100% call and with the same genotype in all MS.
    3 Assign each SNP of samples M1 and M2 a 1 if the genotype has varied from the reference or a 0 if it has not. The SNPs of the M1 and M2 samples that are not in the reference set or that are not 100% called have been discarded.
    I have done all this with perl. What I now have is a text file with the following structure:
    SNP_1 SNP_2 ...
    M1.1 1 0
    M1.2 1 1
    .
    .
    M2.3 0 0

    And that's all folfs!!, I have no idea what I should do now.
    Any help will be welcome because, as you may deduced, I have no idea of ​​working with arrays or statistics.
    Thank you

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