This repository contains analysis pipelines for:
- RNA-seq alignment, quantification, and quality control
- DNA-seq quality control and imputation
- eQTL and sQTL mapping
- Intergrating with GWAS summary result
- Preservation test and robust WGCNA
git clone https://github.com/liusihan/EAS-and-EUR-brain-regulatory-pattern-discovory-and-comparson-pipeline
Rscript pi1.r P.txt
NOTE
: P.txt is a text file with nominal P value per line without header.
bash robust_eQTL.sh sample_size index.txt PEER_factor FDR output_dir raw_counts.txt
- sample_size: the sample size you want to perform eQTL analysis
- index.txt: output file for sample index
- PEER_factor: number of peer hidden factor to collect
- FDR: storey FDR qvalue for adjust P value
- output_dir: prefix of output directory
- raw_counts.txt: raw counts data, each column stand for a sample, each raw stand for a gene
NOTE
: the output_file include three type eQTL results under different mode in QTLtools(nominal/permutation/conditional)