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An approach is described for simulating data sequence, genotype, and phenotype data to study genomic selection and genome-wide association studies (GWAS). The simulation method, implemented in a software package called AlphaDrop, can be used to simulate genomic data and phenotypes with flexibility in terms of the historical population structure, recent pedigree structure, distribution of quantitative trait loci effects, and with sequence and single nucleotide polymorphism-phased alleles and genotypes. Ten replicates of a representative scenario used to study genomic selection in livestock were generated and have been made publically available. The simulated data sets were structured to encompass a spectrum of additive quantitative trait loci effect distributions, relationship structures, and single nucleotide polymorphism chip densities.
Pubmed ID: 22540033
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Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity.
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