ChickenGTEx_pilot_phase

This repository contains codes used in data analysis of the pilot phase of the ChickenGTEx. Codes includes the following sections:

1. RNA-Seq raw data processing
2. Whole genome sequencing raw data processing
3. Single cell RNA-Seq raw data processing
4. Genotype imputation
5. Sample clustering
6. Tissue specificity analysis of gene expression
7. Sex-baised gene expression
8. Molecular quantitative trait locus (molQTL) mapping
9. Analysis of molQTL tissue sharing
10. GWAS colocalization
11. Comparative analysis