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Example 2
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Part 2
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Part 2: Finding SNPs differing between populations and filtering for those that may be phenotype-associated.
Overview:
Sum up allele counts for Caucasians and Africans
Filter the gd_snp datase using a complex expression to get SNPs fixed on opposite alleles
Further filter the SNPs to those in regions of diminished variation through clustering
Finding coding SNPs: using the aaChanges tool
Finding non-coding SNPs: intersecting with ENCODE DNase hypersensitive sites and transcription factor occupied segments
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