This repository contains codes used in data analysis of the pilot phase of the ChickenGTEx. Codes includes the following sections:
- RNA-Seq raw data processing
- Whole genome sequencing raw data processing
- Single cell RNA-Seq raw data processing
- Genotype imputation
- Sample clustering
- Tissue specificity analysis of gene expression
- Sex-baised gene expression
- Molecular quantitative trait locus (molQTL) mapping
- Analysis of molQTL tissue sharing
- GWAS colocalization
- Comparative analysis