Scathacheng / population-compare-pipeline

Analysis pipelines for QTL discovery and GWAS signals interpretation

Analysis pipelines for eQTL/sQTL discovery and GWAS signals interpratation

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
  

Install

git clone https://github.com/liusihan/EAS-and-EUR-brain-regulatory-pattern-discovory-and-comparson-pipeline

Softwares

• R-3.3.3
• QTLtools
• LDSC
• SMR
• PrediXcan

Usage

QTl replicatin rate

Rscript pi1.r P.txt

NOTE: P.txt is a text file with nominal P value per line without header.

Downsampling analysis

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)