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@@ -6,6 +6,6 @@ Allele-Specifc Expression Data From Reference Cohorts Following Best Practices
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Contains Data from the MAGE [study](https://github.com/mccoy-lab/MAGE) spanning 731 individuals from 26 different ancestry groups. Briefly allele-specific expression data (ASE) was generated using high coverage 1000 genomes genotypes and phASER using best [practices](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0762-6). The following archive should contain two CSV files namely:
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* MAGE_ASE/MAGE_varlevel.csv: Containing ASE data aggregated at variant level by choosing the most expressed SNP overlapping each gene (as defined in gencode v26). Variant level ASE was produced from the ```allelic_counts``` file from phASER.
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* MAGE_ASE/MAGE_haplevel.csv: Containing ASE data aggregated at haplotype level using phASER and gencode v26.
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Both files have the same input structure with rows being Genes (identified by ENSEMBL IDs) and columns being the Sample IDs. The values are pairs of (reference, alternate) counts.
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* Both files have the same input structure with rows being Genes (identified by ENSEMBL IDs) and columns being the Sample IDs. The values are pairs of (reference, alternate) counts.
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* Application of ASE Quality Control on the Cohort can be retrieved from our paper [here]()
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