This repository contains the data analysis code used in the manuscript:
Genetic effects on promoter usage are highly context-specific and contribute to complex traits https://doi.org/10.7554/eLife.41673
- analysis - data analysis code
- configs - Snakemake workflow config files
- scripts - Stand-alone scripts used by the Snakemake workflows
- quantify_transcription.snakefile - RNA-seq quantification workflow
- map_QTLs.snakefile - QTL mapping workflow
- run_coloc.snakefile - Colocalisation workflow
- run_fgwas.snakefile - fgwas enrichment workflow
- quantify_simulations.snakefile - Quantify simulated RNA-seq data
- txrevise - https://github.com/kauralasoo/txrevise
- Many functions are imported from the seqUtils package: https://github.com/kauralasoo/seqUtils