smontgomlab/AFGR

Landing page with directions for accessing the African Functional Genomics Resource (AFGR) datasets. # African Functional Genomics Resource (AFGR) The African Functional Genomics Resource includes RNA-seq, expression QTLs (eQTLs), and splicing QTLs (sQTLs) on all 593 individuals, and ATAC-seq and chromatin accessibility QTLs (caQTLs) on a representative 100 individual subset. The populations and their numbers are represented in the map below. eQTLs are defined as `SNP`-`transcript` pairs; sQTLs are `SNP`-`splice junction` pairs; caQTLs are `SNP`-`chromatin region` pairs. # Download QTL Data All QTL summary statistics files will be available in tabixed format in the **AFGR Dropbox** ### eQTLs: ### **AFGR eQTLs** - [x] ESN - [x] GWD - [x] LWK - [x] MSL - [x] YRI - [x] MKK - [x] **Meta-analysis** ### **GEUVADIS eQTLs** *GEUVADIS eQTLs called and meta-analyzed using the same pipeline as AFGR* - [x] CEU - [x] FIN - [x] GBR - [x] TSI - [x] EUR (bulk-called eQTLs across CEU, FIN, GBR, and TSI) - [x] **Meta-analysis** (meta-analysis of CEU, FIN, GBR, and TSI eQTLs) - [x] YRI ### sQTLs: **AFGR sQTLs** - [x] ESN - [x] GWD - [x] LWK - [x] MSL - [x] YRI - [x] MKK - [x] **Meta-analysis** ### caQTLs: **AFGR caQTLs** - [x] AFR (called in bulk using ATAC-seq data from 100 samples spanning all 6 population groups) # Access RNA-seq and ATAC-seq Data The RNA-seq and ATAC-seq tracks will be available at **ENCODE** soon.