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Frequently Asked Questions
How can I join DEEP with my cohort?
What if I have multiple datasets to process?
What if I have a dataset with both 450k and EPIC?
What if I have a dataset with both EPICv1 and EPICv2?
What if I have a dataset with a case control design?
What if I have a dataset where DNA methylation has been measured at multiple timepoints?
What if I am not allowed to impute my dataset on an external server?
Can other collaborators download my results?
Do I need to have chromosome X in my data?
I don't have rights to install any software myself can I still run the pipeline?
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- Frequently Asked Questions
- Participation requirements
- Submit an issue or start a discussion
- System requirements and pipeline installation
0. Set up folders
1a. Check data
1b. Process genetic data
1c. Check methylation and phenotypes
1d. mQTL control GWAS
1e. GWAS of genetic PCs
1f. Cross-cohort normalisation of methylation data
1g. Compute haplotype components
1 upload. Upload to Bristol SFTP
2a. Relatedness assessment/removal
2b. Regular and variance EWAS
3a. Run meQTL analysis
3b. Run variance meQTL analysis