MSBB brain gene expression QTL#

Contact#

Minghui Wang

Links to QTL analysis notebooks#

See notebooks in:

• https://github.com/cumc/xqtl-analysis/tree/main/analysis/Wang_Columbia/MSBB/eQTL

The notebooks in this folder contain the commands and data wrangling codes for analysis of the expression data in MSBB. (data wrangling exist because not all data are processed using the xqtl-pipeline from the beginning and need to be reformatted to fit one intermediate step of the pipeline).

Association data preprocessing#

Genotype data preprocessing#

Principal component analysis for eQTL mapping#

Phenotype data preprocessing#

Covariate data preprocessing#

Association scan using TensorQTL and summary statistics standardization#

• TensorQTL.ipynb provides the pipeline to generate TensorQTL cis association results for all QTLs.
• MSBB_eQTL provides information about the input files for TensorQTL cis association in the base_params variable in [generate_command_1].

Path(s) to cis-QTL association testing#

output of TensorQTL.ipynb

• s3://statfungen/ftp_fgc_xqtl/analysis_result/cis_association/MSBB/eQTL/