STARNET macrophage gene expression QTL#

STARNET is an RNA expression study of various disease-relevant tissues obtained from living patients with cardiovascular disease (CVD). The inclusion criterion for patients was eligibility for coronary artery by-pass graft (CABG) surgery. Please refer to this document for an overview of the STARNET project.

Contact#

  • Contact Name: Travyse Edwards
  • Contact Email: travyse.edwards@icahn.mssm.edu
  • Contact Affiliation: Icahn School of Medicine at Mount Sinai
  • Contact Role: Travyse performed QC & QTL analysis

Study Overview#

  • Study name : STARNET Macrophage eQTL
  • Study Description : Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task (STARNET) macrophage eQTL analysis summary statistics generated using the FGC xQTL pipeline.

Analysis Details#

Sample Size Tracking Through Analysis Workflow#

StepSample Size
Raw Expression Data480
QC’d Expression Data479
After overlapping with STARNET genotype data471

Quality Control and Normalization Details for Phenotype Data#

For quality control performed for the macrophage gene expression dataset, please refer to this markdown document.

Genotype Parameters#

ParameterValue
Minimum Minor Allele Freq0.01
Maximum Minor Allele Freq0.99
Kinship Coefficient for Related Individuals0.0625
Maximum Missingness Per Variant0.1
Maximum Missingness Per Sample0.1
Hardy-Weinberg Equilibrium Filter1e-15

Covariate Parameters#

PCA Analysis:

ParameterValue
Minor Allele Freq for PCA0.01
LD Pruning: Window0.1
LD Pruning: Shift0.1
LD Pruning: Window0.1
Number of PCs13

PEER Analysis:

ParameterValue
Max Iterations1000
Prior Parameter: Alpha_a0.001
Prior Parameter: Alpha_b0.1
Prior Parameter: Eps_a0.1
Prior Parameter: Eps_b10.0
Tolerance Parameter: tol0.001
Tolerance Parameter: var_tol1e-5
Convergence Mode“fast”

Final Covariates: Sex, Age, PCs (13), PEER Factors (60)

PCA Method for Latent Factor Identification (Using Marchenko-Pastur Method):

TBD

TensorQTL Parameters#

ParameterValue
Cis Window1,000,000
Minor Allele Count Cutoff0
Minor Allele Freq Cutoff0

Currently rearranging this section and below

The notebooks in this folder,

https://github.com/cumc/fungen-xqtl-analysis/tree/main/analysis/Marcora_MSSM/STARNET

contain the commands and some of the results visualizations produced by the pipeline when analyzing the STARNET macrophage RNA-seq expression data.

  • STARNET_Analysis_Complete.ipynb provides information about the imputation of genotype, summary from other preprocessing steps, and a look into the cisQTL association scan.
  • genotype_preprocessing.ipynb shows the commands used for genotype processing and preparation steps.
    • Mostly contains the commands used to run the pipeline, but includes some pre-pipeline data wrangling.
    • This includes QC, PCA, and GRM steps
  • phenotype_preprocessing.ipynb shows the commands used for the phenotype data processing and preparation steps.
    • As above, it mostly contains the commands used to run the pipeline, but includes some pre-pipeline data wrangling.
    • This includes quantification steps, QC, annotation, and residual expression steps
  • covariate_preprocessing.ipynb shows the commands used for the covariate data processing and preparation steps.
    • This includes factor analysis steps
  • association_scan_cis.ipynb provides information about the TensorQTL cis association scan.

Wang lab:

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

Dataset Details#

  • Number of cases :
  • Number of controls :
  • Annotation information :
  • Genotype level imputation :
  • Imputation Panel :

Path(s) to Genotype Matrix#

  • Goate Lab (Minerva), /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/
$ ls -lh /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/*.{bed,bim,fam}
-rw-r-xr--+ 1 edwart10 LOAD  58M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.10.bed
-rw-r-xr--+ 1 edwart10 LOAD  19M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.10.bim
-rw-r-xr--+ 1 edwart10 LOAD  14K May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.10.fam
-rw-r-xr--+ 1 edwart10 LOAD  57M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.11.bed
-rw-r-xr--+ 1 edwart10 LOAD  18M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.11.bim
-rw-r-xr--+ 1 edwart10 LOAD  14K May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.11.fam
-rw-r-xr--+ 1 edwart10 LOAD  55M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.12.bed
-rw-r-xr--+ 1 edwart10 LOAD  18M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.12.bim
-rw-r-xr--+ 1 edwart10 LOAD  14K May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.12.fam
-rw-r-xr--+ 1 edwart10 LOAD  43M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.13.bed
-rw-r-xr--+ 1 edwart10 LOAD  14M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.13.bim
-rw-r-xr--+ 1 edwart10 LOAD  14K May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.13.fam
-rw-r-xr--+ 1 edwart10 LOAD  37M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.14.bed
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-rw-r-xr--+ 1 edwart10 LOAD  11M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.15.bim
-rw-r-xr--+ 1 edwart10 LOAD  14K May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.15.fam
-rw-r-xr--+ 1 edwart10 LOAD  35M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.16.bed
-rw-r-xr--+ 1 edwart10 LOAD  11M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.16.bim
-rw-r-xr--+ 1 edwart10 LOAD  14K May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.16.fam
-rw-r-xr--+ 1 edwart10 LOAD  31M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.17.bed
-rw-r-xr--+ 1 edwart10 LOAD 9.5M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.17.bim
-rw-r-xr--+ 1 edwart10 LOAD  14K May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.17.fam
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-rw-r-xr--+ 1 edwart10 LOAD  14K May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.18.fam
-rw-r-xr--+ 1 edwart10 LOAD  26M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.19.bed
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-rw-r-xr--+ 1 edwart10 LOAD  89M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.1.bed
-rw-r-xr--+ 1 edwart10 LOAD  28M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.1.bim
-rw-r-xr--+ 1 edwart10 LOAD  14K May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.1.fam
-rw-r-xr--+ 1 edwart10 LOAD  26M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.20.bed
-rw-r-xr--+ 1 edwart10 LOAD 8.0M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.20.bim
-rw-r-xr--+ 1 edwart10 LOAD  14K May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.20.fam
-rw-r-xr--+ 1 edwart10 LOAD  16M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.21.bed
-rw-r-xr--+ 1 edwart10 LOAD 4.9M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.21.bim
-rw-r-xr--+ 1 edwart10 LOAD  14K May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.21.fam
-rw-r-xr--+ 1 edwart10 LOAD  16M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.22.bed
-rw-r-xr--+ 1 edwart10 LOAD 4.8M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.22.bim
-rw-r-xr--+ 1 edwart10 LOAD  14K May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.22.fam
-rw-r-xr--+ 1 edwart10 LOAD  96M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.2.bed
-rw-r-xr--+ 1 edwart10 LOAD  30M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.2.bim
-rw-r-xr--+ 1 edwart10 LOAD  14K May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.2.fam
-rw-r-xr--+ 1 edwart10 LOAD  81M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.3.bed
-rw-r-xr--+ 1 edwart10 LOAD  25M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.3.bim
-rw-r-xr--+ 1 edwart10 LOAD  14K May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.3.fam
-rw-r-xr--+ 1 edwart10 LOAD  83M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.4.bed
-rw-r-xr--+ 1 edwart10 LOAD  26M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.4.bim
-rw-r-xr--+ 1 edwart10 LOAD  14K May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.4.fam
-rw-r-xr--+ 1 edwart10 LOAD  74M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.5.bed
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-rw-r-xr--+ 1 edwart10 LOAD  24M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.6.bim
-rw-r-xr--+ 1 edwart10 LOAD  14K May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.6.fam
-rw-r-xr--+ 1 edwart10 LOAD  67M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.7.bed
-rw-r-xr--+ 1 edwart10 LOAD  21M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.7.bim
-rw-r-xr--+ 1 edwart10 LOAD  14K May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.7.fam
-rw-r-xr--+ 1 edwart10 LOAD  63M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.8.bed
-rw-r-xr--+ 1 edwart10 LOAD  19M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.8.bim
-rw-r-xr--+ 1 edwart10 LOAD  14K May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.8.fam
-rw-r-xr--+ 1 edwart10 LOAD  50M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.9.bed
-rw-r-xr--+ 1 edwart10 LOAD  15M May 28  2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.9.bim
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Path(s) to Phenotype Matrix#

  • Goate lab, /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/
$ ls -lh /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/*.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 1.8M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr10.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 2.5M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr11.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 2.5M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr12.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 842K Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr13.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 1.6M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr14.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 1.6M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr15.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 2.3M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr16.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 2.8M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr17.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 723K Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr18.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 3.0M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr19.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 4.6M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr1.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 1.2M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr20.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 489K Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr21.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 1.2M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr22.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 3.0M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr2.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 2.5M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr3.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 1.6M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr4.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 2.0M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr5.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 2.4M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr6.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 2.2M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr7.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 1.6M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr8.bed.gz
-rw-r-xr--+ 1 edwart10 LOAD 1.8M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr9.bed.gz

Path(s) to Covariate Matrix#

  • Goate lab, /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/no-status/data-preprocessing/covariates/STARNET.MP.cov.merged.gz
-rw-r-x---+ 1 edwart10 LOAD 204K May  4 09:57 STARNET.MP.cov.merged.gz

Path(s) to cis-eQTL Results#

  • Goate lab, /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/no-status/association_scan/TensorQTL/Marchenko-Pastur-Method
$ ls -lh *.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 995M May  6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.10.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 1.3G May  6 11:49 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.11.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 1.4G May  6 11:48 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.12.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 516M May  6 11:45 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.13.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 908M May  6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.14.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 820M May  6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.15.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 1.3G May  6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.16.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 1.5G May  6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.17.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 452M May  6 11:45 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.18.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 1.8G May  6 11:47 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.19.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 2.3G May  6 11:47 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.1.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 638M May  6 11:45 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.20.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 282M May  6 11:45 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.21.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 636M May  6 11:45 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.22.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 1.6G May  6 11:47 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.2.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 1.4G May  6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.3.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 935M May  6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.4.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 1.1G May  6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.5.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 1.7G May  6 11:47 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.6.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 1.2G May  6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.7.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 915M May  6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.8.norminal.cis_long_table.txt
-rw-r-xr--+ 1 edwart10 LOAD 922M May  6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.9.norminal.cis_long_table.txt

Path(s) to cis-QTL association testing#

output of TensorQTL.ipynb

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

Path(s) to Fine-Mapping via SuSiE#

TBD

Path(s) to Fine-Mapping via SuSiE-RSS#

TBD