HSrats-ADDO-sQTL

This is a pipeline used for the splicing QTL analysis based on the RNA-seq data of HSrats fat and liver tissues.

STEP1. Convert the gene/transcript expression levels to the input format required by ADDO.

STEP2. eQTL mapping based on ADDO using the gene/transcript expression levels of two tissues.

STEP3. Summary the peak eQTLs from the ADDO GWAS results.

STEP4. Summary the corresponding pairs between gene-based eQTLs and transcript-based eQTLs and find the antagonistic/synergistic eQTL pairs.

STEP5. Summary the proportions of different eQTL types and calculate the significance of dominance enrichment among trans-eQTLs.

Name		Name	Last commit message	Last commit date
Latest commit History 4 Commits
1-RawData_RUN.sh		1-RawData_RUN.sh
1-RawData_RUN_fat.r		1-RawData_RUN_fat.r
1-RawData_RUN_liver.r		1-RawData_RUN_liver.r
2-Fat_G-GWAS_AddDom_Model.r		2-Fat_G-GWAS_AddDom_Model.r
2-Fat_G-GWAS_AddDom_Model_EMMA.r		2-Fat_G-GWAS_AddDom_Model_EMMA.r
2-Fat_T-GWAS_AddDom_Model.r		2-Fat_T-GWAS_AddDom_Model.r
2-Fat_T-GWAS_AddDom_Model_EMMA.r		2-Fat_T-GWAS_AddDom_Model_EMMA.r
2-Liver_G-GWAS_AddDom_Model.r		2-Liver_G-GWAS_AddDom_Model.r
2-Liver_G-GWAS_AddDom_Model_EMMA.r		2-Liver_G-GWAS_AddDom_Model_EMMA.r
2-Liver_T-GWAS_AddDom_Model.r		2-Liver_T-GWAS_AddDom_Model.r
2-Liver_T-GWAS_AddDom_Model_EMMA.r		2-Liver_T-GWAS_AddDom_Model_EMMA.r
3-SNP_Peak_RUN.r		3-SNP_Peak_RUN.r
3-SNP_Peak_RUN_new.r		3-SNP_Peak_RUN_new.r
4-sQTL_Summary_Fat.r		4-sQTL_Summary_Fat.r
4-sQTL_Summary_Fat_examples.r		4-sQTL_Summary_Fat_examples.r
4-sQTL_Summary_Liver.r		4-sQTL_Summary_Liver.r
4-sQTL_Summary_Liver_examples.r		4-sQTL_Summary_Liver_examples.r
4-sQTL_Summary_Plot_Fat.r		4-sQTL_Summary_Plot_Fat.r
4-sQTL_Summary_Plot_Liver.r		4-sQTL_Summary_Plot_Liver.r
5-eQTL_Ratio_Summary.r		5-eQTL_Ratio_Summary.r
README.md		README.md

Provide feedback