MAGENTA African American Blood Gene Expression QTL #

Multi-Ancestry Genomics, Epigenomics, and Transcriptomics of Alzheimer’s (MAGENTA) Project: Participants include 465 individuals (AA – 113 with AD, 118 cognitively intact controls; NHW – 116 with AD, 118 controls) ascertained by the John P. Hussman Institute for Human Genomics (HIHG) at the University of Miami Miller School of Medicine (Miami, FL), North Carolina A&T State University (Greensboro, NC), and Case Western Reserve University (Cleveland, OH). Participants were ascertained as part of the ADSP Follow-up Study and included both cases (>65 years of age of onset) and controls (>65 years of age at age of exam). All participants were adjudicated by a clinical panel with expertise in AD related disorders and classified as AD according to standard criteria developed by the National Institute of Aging and the Alzheimer’s Association.

Contact #

Makaela Mews (analyst; mxm1368@case.edu); Dr. William S. Bush ( wsb36@case.edu); Dr. Anthony J. Griswold (Griswold, Anthony J agriswold@miami.edu)

Study Overview #

Sample information: MAGENTA/MAGENTA_AA_eqtl_sample_attributes.csv.
Lab protocol: MAGENTA/MAGENTA_AA_eqtl_lab_protocol.csv.
Computational protocol: MAGENTA/MAGENTA_AA_eqtl_computational_protocol.csv.
QTL summary statistics output: MAGENTA/MAGENTA_AA_expression.qtl_results.csv.
Fine-mapping results individual level data model: ####/####.susie.csv.
Fine-mapping results summary statistics model: ####/####.susie_rss.csv.
Colocalization with AD GWAS: ####/####.susie_coloc.csv. where “Sample information” is a CSV file containing sample attributes / complete set of covariates for the exact samples used in the QTL study; “Lab protocol” is a CSV file containing the experimental protocol information to process the samples; “Computational protocol” is a CSV file containing the computational protocol information to process the samples; “QTL summary statistics output” is the list of QTL summary statistics results; “Fine-mapping results individual level data model” is the list of fine-mapped QTL using individual level phenotype and genotype data input for SuSiE model. “Fine-mapping results summary statistics model” uses QTL summary statistics for SuSiE RSS model. “Colocalization with AD GWAS” is the list of colocalization analysis with different AD GWAS publications and data-sets using coloc model on SuSiE results.

Analysis Status #

TransQTL association: Need to be updated with new covariate files.

Dataset Details #

Path(s) to genotype matrix #

Here please document the exact genotype matrix used for QTL calling.

Path(s) to the data on your local cluster where you analyzed the data.
TensorQTL - cis: Bush Lab, server: rider.case.edu /mnt/pan/Data14/metabrain_lasso/rna_seq_norm/aa_233/geno/by_chr/aa_chr1_22.no_rel.filtered.plink_files_list.txt
TensorQTL - trans: Bush Lab, server: rider.case.edu /mnt/pan/Data14/metabrain_lasso/rna_seq_norm/aa_233/geno/geno_final/aa_chr1_22.no_rel.filtered.bed
NIAGADS FTP, /ftp_fgc_xqtl/projects/... A summary of the genotype data including size used for TensorQTL - cis:

$ ls -lh *{bed,bim,fam,txt}
-rw-r--r-- 1 mxm1368 wsb36  31M Mar 23 14:41 aa_chr1_22.no_rel.filtered.10.bed
-rw-r--r-- 1 mxm1368 wsb36  21M Mar 23 14:41 aa_chr1_22.no_rel.filtered.10.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.10.fam
-rw-r--r-- 1 mxm1368 wsb36  30M Mar 23 14:41 aa_chr1_22.no_rel.filtered.11.bed
-rw-r--r-- 1 mxm1368 wsb36  20M Mar 23 14:41 aa_chr1_22.no_rel.filtered.11.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.11.fam
-rw-r--r-- 1 mxm1368 wsb36  30M Mar 23 14:41 aa_chr1_22.no_rel.filtered.12.bed
-rw-r--r-- 1 mxm1368 wsb36  20M Mar 23 14:41 aa_chr1_22.no_rel.filtered.12.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.12.fam
-rw-r--r-- 1 mxm1368 wsb36  24M Mar 23 14:41 aa_chr1_22.no_rel.filtered.13.bed
-rw-r--r-- 1 mxm1368 wsb36  16M Mar 23 14:41 aa_chr1_22.no_rel.filtered.13.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.13.fam
-rw-r--r-- 1 mxm1368 wsb36  21M Mar 23 14:41 aa_chr1_22.no_rel.filtered.14.bed
-rw-r--r-- 1 mxm1368 wsb36  14M Mar 23 14:41 aa_chr1_22.no_rel.filtered.14.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.14.fam
-rw-r--r-- 1 mxm1368 wsb36  18M Mar 23 14:41 aa_chr1_22.no_rel.filtered.15.bed
-rw-r--r-- 1 mxm1368 wsb36  12M Mar 23 14:41 aa_chr1_22.no_rel.filtered.15.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.15.fam
-rw-r--r-- 1 mxm1368 wsb36  20M Mar 23 14:41 aa_chr1_22.no_rel.filtered.16.bed
-rw-r--r-- 1 mxm1368 wsb36  13M Mar 23 14:41 aa_chr1_22.no_rel.filtered.16.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.16.fam
-rw-r--r-- 1 mxm1368 wsb36  17M Mar 23 14:41 aa_chr1_22.no_rel.filtered.17.bed
-rw-r--r-- 1 mxm1368 wsb36  11M Mar 23 14:41 aa_chr1_22.no_rel.filtered.17.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.17.fam
-rw-r--r-- 1 mxm1368 wsb36  19M Mar 23 14:41 aa_chr1_22.no_rel.filtered.18.bed
-rw-r--r-- 1 mxm1368 wsb36  12M Mar 23 14:41 aa_chr1_22.no_rel.filtered.18.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.18.fam
-rw-r--r-- 1 mxm1368 wsb36  13M Mar 23 14:41 aa_chr1_22.no_rel.filtered.19.bed
-rw-r--r-- 1 mxm1368 wsb36 7.9M Mar 23 14:41 aa_chr1_22.no_rel.filtered.19.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.19.fam
-rw-r--r-- 1 mxm1368 wsb36  49M Mar 23 14:41 aa_chr1_22.no_rel.filtered.1.bed
-rw-r--r-- 1 mxm1368 wsb36  31M Mar 23 14:41 aa_chr1_22.no_rel.filtered.1.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.1.fam
-rw-r--r-- 1 mxm1368 wsb36  15M Mar 23 14:41 aa_chr1_22.no_rel.filtered.20.bed
-rw-r--r-- 1 mxm1368 wsb36 9.1M Mar 23 14:41 aa_chr1_22.no_rel.filtered.20.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.20.fam
-rw-r--r-- 1 mxm1368 wsb36 8.9M Mar 23 14:41 aa_chr1_22.no_rel.filtered.21.bed
-rw-r--r-- 1 mxm1368 wsb36 5.8M Mar 23 14:41 aa_chr1_22.no_rel.filtered.21.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.21.fam
-rw-r--r-- 1 mxm1368 wsb36 7.9M Mar 23 14:41 aa_chr1_22.no_rel.filtered.22.bed
-rw-r--r-- 1 mxm1368 wsb36 5.2M Mar 23 14:41 aa_chr1_22.no_rel.filtered.22.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.22.fam
-rw-r--r-- 1 mxm1368 wsb36  53M Mar 23 14:41 aa_chr1_22.no_rel.filtered.2.bed
-rw-r--r-- 1 mxm1368 wsb36  34M Mar 23 14:41 aa_chr1_22.no_rel.filtered.2.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.2.fam
-rw-r--r-- 1 mxm1368 wsb36  45M Mar 23 14:41 aa_chr1_22.no_rel.filtered.3.bed
-rw-r--r-- 1 mxm1368 wsb36  29M Mar 23 14:41 aa_chr1_22.no_rel.filtered.3.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.3.fam
-rw-r--r-- 1 mxm1368 wsb36  45M Mar 23 14:41 aa_chr1_22.no_rel.filtered.4.bed
-rw-r--r-- 1 mxm1368 wsb36  28M Mar 23 14:41 aa_chr1_22.no_rel.filtered.4.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.4.fam
-rw-r--r-- 1 mxm1368 wsb36  40M Mar 23 14:41 aa_chr1_22.no_rel.filtered.5.bed
-rw-r--r-- 1 mxm1368 wsb36  25M Mar 23 14:41 aa_chr1_22.no_rel.filtered.5.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.5.fam
-rw-r--r-- 1 mxm1368 wsb36  41M Mar 23 14:41 aa_chr1_22.no_rel.filtered.6.bed
-rw-r--r-- 1 mxm1368 wsb36  26M Mar 23 14:41 aa_chr1_22.no_rel.filtered.6.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.6.fam
-rw-r--r-- 1 mxm1368 wsb36  36M Mar 23 14:41 aa_chr1_22.no_rel.filtered.7.bed
-rw-r--r-- 1 mxm1368 wsb36  22M Mar 23 14:41 aa_chr1_22.no_rel.filtered.7.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.7.fam
-rw-r--r-- 1 mxm1368 wsb36  36M Mar 23 14:41 aa_chr1_22.no_rel.filtered.8.bed
-rw-r--r-- 1 mxm1368 wsb36  23M Mar 23 14:41 aa_chr1_22.no_rel.filtered.8.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.8.fam
-rw-r--r-- 1 mxm1368 wsb36  28M Mar 23 14:41 aa_chr1_22.no_rel.filtered.9.bed
-rw-r--r-- 1 mxm1368 wsb36  18M Mar 23 14:41 aa_chr1_22.no_rel.filtered.9.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.9.fam
-rw-r--r-- 1 mxm1368 wsb36 2.2K Mar 23 14:41 aa_chr1_22.no_rel.filtered.plink_files_list.txt

A summary of the genotype data including size used for TensorQTL - trans:

$ ls -lh aa_chr1_22.no_rel.filtered.{bim,bed,fam}
-rw-r--r-- 1 mxm1368 wsb36 619M Mar 23 14:41 aa_chr1_22.no_rel.filtered.bed
-rw-r--r-- 1 mxm1368 wsb36 394M Mar 23 14:41 aa_chr1_22.no_rel.filtered.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:41 aa_chr1_22.no_rel.filtered.fam

Path(s) to omics-data matrix #

Here please document the exact omics-data matrix used for QTL calling.

Path(s) to the data on your local cluster where you analyzed the data.
TensorQTL - cis: Bush Lab, server: rider.case.edu /mnt/pan/Data14/metabrain_lasso/rna_seq_norm/aa_233/mol_phe/tmm_per_chr/
TensorQTL - trans: Bush Lab, server: rider.case.edu /mnt/pan/Data14/metabrain_lasso/rna_seq_norm/aa_233/mol_phe
NIAGADS FTP, /ftp_fgc_xqtl/projects/... A summary of the phenotype data including size used for TensorQTL - cis:

$ pwd
/mnt/pan/Data14/metabrain_lasso/rna_seq_norm/aa_233/mol_phe/tmm_per_chr
$ ls -lh *.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 469K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr10.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 689K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr11.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 689K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr12.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 216K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr13.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 494K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr14.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 416K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr15.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 665K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr16.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 828K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr17.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 186K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr18.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 969K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr19.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 1.3M Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr1.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 334K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr20.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 138K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr21.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 373K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr22.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 842K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr2.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 675K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr3.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 426K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr4.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 552K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr5.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 649K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr6.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 663K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr7.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 421K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr8.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 487K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr9.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 399K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chrX.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  12K Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chrY.bed.gz

A summary of the phenotype data including size used for TensorQTL - trans:

$ pwd
/mnt/pan/Data14/metabrain_lasso/rna_seq_norm/aa_233/mol_phe
$ ls -lh *tmm.expression.bed.gz
-rw-r----- 1 mxm1368 wsb36 13M Feb 27 17:55 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.gz

Path(s) to covariate data matrix #

Here please document the exact covariate matrix used for QTL calling, including selected covariates from sample attribute file, genotype PC and phenotype hidden confounding factors computed in your previous analysis

Path(s) to the data on your local cluster where you analyzed the data.
Bush Lab, server: rider.case.edu /mnt/pan/Data14/metabrain_lasso/rna_seq_norm/aa_233/cov/
NIAGADS FTP, /ftp_fgc_xqtl/projects/... A summary of the covariate data including size used for TensorQTL - cis & trans:

$ ls -lh *tmm.expression.cov_pca.resid.PEER.cov.gz
-rw-r--r-- 1 mxm1368 wsb36 85K Feb 27 18:04 aa_no_rel.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.cov_pca.resid.PEER.cov.gz

Path(s) to QTL results #

TensorQTL - cis: Bush Lab, server: rider.case.edu /mnt/pan/Data14/metabrain_lasso/rna_seq_norm/aa_233/tensorqtl/cis/plink_mac5
TensorQTL - trans: Bush Lab, server: rider.case.edu /mnt/pan/Data14/metabrain_lasso/rna_seq_norm/aa_233/tensorqtl/trans/plink_mac5 A summary of the TensorQTL - cis data including size:

$ ls -lh
total 34G
-rw-r--r-- 1 mxm1368 wsb36 177M Mar 23 15:48 aa_no_rel.10.cis_qtl_pairs.10.parquet
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 23 16:51 aa_no_rel.10.cis_qtl_pairs.10.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  52K Mar 23 16:51 aa_no_rel.10.cis_qtl_pairs.10.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 169K Mar 23 16:51 aa_no_rel.10.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 970M Mar 23 15:53 aa_no_rel.10.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 229M Mar 23 15:03 aa_no_rel.11.cis_qtl_pairs.11.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 16:31 aa_no_rel.11.cis_qtl_pairs.11.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  78K Mar 23 16:31 aa_no_rel.11.cis_qtl_pairs.11.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 247K Mar 23 16:31 aa_no_rel.11.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.3G Mar 23 15:09 aa_no_rel.11.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 241M Mar 23 16:51 aa_no_rel.12.cis_qtl_pairs.12.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 17:55 aa_no_rel.12.cis_qtl_pairs.12.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  79K Mar 23 17:55 aa_no_rel.12.cis_qtl_pairs.12.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 248K Mar 23 17:55 aa_no_rel.12.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.4G Mar 23 16:58 aa_no_rel.12.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36  84M Mar 23 16:13 aa_no_rel.13.cis_qtl_pairs.13.parquet
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 23 16:42 aa_no_rel.13.cis_qtl_pairs.13.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  24K Mar 23 16:42 aa_no_rel.13.cis_qtl_pairs.13.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36  78K Mar 23 16:42 aa_no_rel.13.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 454M Mar 23 16:15 aa_no_rel.13.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 186M Mar 23 14:59 aa_no_rel.14.cis_qtl_pairs.14.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 16:06 aa_no_rel.14.cis_qtl_pairs.14.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  55K Mar 23 16:06 aa_no_rel.14.cis_qtl_pairs.14.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 178K Mar 23 16:06 aa_no_rel.14.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.1G Mar 23 15:03 aa_no_rel.14.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 145M Mar 23 15:51 aa_no_rel.15.cis_qtl_pairs.15.parquet
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 23 16:45 aa_no_rel.15.cis_qtl_pairs.15.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  46K Mar 23 16:45 aa_no_rel.15.cis_qtl_pairs.15.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 151K Mar 23 16:45 aa_no_rel.15.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 778M Mar 23 15:56 aa_no_rel.15.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 214M Mar 23 15:02 aa_no_rel.16.cis_qtl_pairs.16.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 16:25 aa_no_rel.16.cis_qtl_pairs.16.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  76K Mar 23 16:25 aa_no_rel.16.cis_qtl_pairs.16.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 238K Mar 23 16:25 aa_no_rel.16.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.2G Mar 23 15:08 aa_no_rel.16.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 253M Mar 23 17:13 aa_no_rel.17.cis_qtl_pairs.17.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 18:02 aa_no_rel.17.cis_qtl_pairs.17.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  92K Mar 23 18:02 aa_no_rel.17.cis_qtl_pairs.17.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 289K Mar 23 18:02 aa_no_rel.17.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.4G Mar 23 17:18 aa_no_rel.17.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36  72M Mar 23 14:51 aa_no_rel.18.cis_qtl_pairs.18.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 15:11 aa_no_rel.18.cis_qtl_pairs.18.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  20K Mar 23 15:11 aa_no_rel.18.cis_qtl_pairs.18.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36  63K Mar 23 15:11 aa_no_rel.18.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 382M Mar 23 14:52 aa_no_rel.18.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 347M Mar 23 15:10 aa_no_rel.19.cis_qtl_pairs.19.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 17:17 aa_no_rel.19.cis_qtl_pairs.19.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36 110K Mar 23 17:17 aa_no_rel.19.cis_qtl_pairs.19.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 346K Mar 23 17:17 aa_no_rel.19.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.9G Mar 23 15:20 aa_no_rel.19.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 415M Mar 23 15:18 aa_no_rel.1.cis_qtl_pairs.1.parquet
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 23 17:44 aa_no_rel.1.cis_qtl_pairs.1.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36 147K Mar 23 17:44 aa_no_rel.1.cis_qtl_pairs.1.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 459K Mar 23 17:44 aa_no_rel.1.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 2.3G Mar 23 15:30 aa_no_rel.1.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 115M Mar 23 14:54 aa_no_rel.20.cis_qtl_pairs.20.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 15:33 aa_no_rel.20.cis_qtl_pairs.20.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  36K Mar 23 15:33 aa_no_rel.20.cis_qtl_pairs.20.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 117K Mar 23 15:33 aa_no_rel.20.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 621M Mar 23 14:57 aa_no_rel.20.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36  58M Mar 23 16:30 aa_no_rel.21.cis_qtl_pairs.21.parquet
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 23 16:49 aa_no_rel.21.cis_qtl_pairs.21.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  15K Mar 23 16:49 aa_no_rel.21.cis_qtl_pairs.21.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36  48K Mar 23 16:49 aa_no_rel.21.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 299M Mar 23 16:32 aa_no_rel.21.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 116M Mar 23 14:55 aa_no_rel.22.cis_qtl_pairs.22.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 15:39 aa_no_rel.22.cis_qtl_pairs.22.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  41K Mar 23 15:39 aa_no_rel.22.cis_qtl_pairs.22.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 133K Mar 23 15:39 aa_no_rel.22.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 667M Mar 23 14:58 aa_no_rel.22.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 286M Mar 23 15:35 aa_no_rel.2.cis_qtl_pairs.2.parquet
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 23 17:18 aa_no_rel.2.cis_qtl_pairs.2.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  96K Mar 23 17:18 aa_no_rel.2.cis_qtl_pairs.2.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 302K Mar 23 17:18 aa_no_rel.2.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.6G Mar 23 15:43 aa_no_rel.2.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 227M Mar 23 17:05 aa_no_rel.3.cis_qtl_pairs.3.parquet
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 23 17:58 aa_no_rel.3.cis_qtl_pairs.3.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  77K Mar 23 17:58 aa_no_rel.3.cis_qtl_pairs.3.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 242K Mar 23 17:58 aa_no_rel.3.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.3G Mar 23 17:11 aa_no_rel.3.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 152M Mar 23 16:14 aa_no_rel.4.cis_qtl_pairs.4.parquet
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 23 17:10 aa_no_rel.4.cis_qtl_pairs.4.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  47K Mar 23 17:10 aa_no_rel.4.cis_qtl_pairs.4.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 153K Mar 23 17:10 aa_no_rel.4.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 856M Mar 23 16:19 aa_no_rel.4.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 192M Mar 23 16:58 aa_no_rel.5.cis_qtl_pairs.5.parquet
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 23 17:50 aa_no_rel.5.cis_qtl_pairs.5.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  61K Mar 23 17:50 aa_no_rel.5.cis_qtl_pairs.5.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 198K Mar 23 17:50 aa_no_rel.5.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.1G Mar 23 17:04 aa_no_rel.5.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 294M Mar 23 17:08 aa_no_rel.6.cis_qtl_pairs.6.parquet
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 23 18:01 aa_no_rel.6.cis_qtl_pairs.6.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  74K Mar 23 18:01 aa_no_rel.6.cis_qtl_pairs.6.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 233K Mar 23 18:01 aa_no_rel.6.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.7G Mar 23 17:16 aa_no_rel.6.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 218M Mar 23 15:02 aa_no_rel.7.cis_qtl_pairs.7.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 16:25 aa_no_rel.7.cis_qtl_pairs.7.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  75K Mar 23 16:25 aa_no_rel.7.cis_qtl_pairs.7.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 238K Mar 23 16:25 aa_no_rel.7.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.2G Mar 23 15:07 aa_no_rel.7.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 170M Mar 23 16:39 aa_no_rel.8.cis_qtl_pairs.8.parquet
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 23 17:30 aa_no_rel.8.cis_qtl_pairs.8.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  47K Mar 23 17:30 aa_no_rel.8.cis_qtl_pairs.8.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 152K Mar 23 17:30 aa_no_rel.8.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 904M Mar 23 16:44 aa_no_rel.8.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 178M Mar 23 14:58 aa_no_rel.9.cis_qtl_pairs.9.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 16:00 aa_no_rel.9.cis_qtl_pairs.9.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  52K Mar 23 16:00 aa_no_rel.9.cis_qtl_pairs.9.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 169K Mar 23 16:00 aa_no_rel.9.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 944M Mar 23 15:02 aa_no_rel.9.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36  100 Mar 23 18:02 aa_no_rel.emprical.cis_sumstats.summary
-rw-r--r-- 1 mxm1368 wsb36 5.9M Mar 23 18:02 aa_no_rel.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36  311 Mar 23 18:02 TensorQTL.cis._column_info.txt
-rw-r--r-- 1 mxm1368 wsb36 5.0K Mar 23 18:02 TensorQTL.cis._recipe.tsv
-rw-r--r-- 1 mxm1368 wsb36  18K Mar 23 18:02 TensorQTL.cis._recipe.tsv.stderr
-rw-r--r-- 1 mxm1368 wsb36   46 Mar 23 18:02 TensorQTL.cis._recipe.tsv.stdout

A summary of the TensorQTL - trans data including size:

$ ls -lh
total 5.1M
-rw-r--r-- 1 mxm1368 wsb36 3.7M Mar 24 09:41 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.norminal.trans_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 24 09:41 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.norminal.trans_long_table.txt.stderr
-rw-r--r-- 1 mxm1368 wsb36  68K Mar 24 09:41 aa_233_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.norminal.trans_long_table.txt.stdout
-rw-r--r-- 1 mxm1368 wsb36  189 Mar 24 09:41 TensorQTL.trans._column_info.txt
-rw-r--r-- 1 mxm1368 wsb36  324 Mar 24 09:41 TensorQTL.trans._recipe.tsv

Path(s) to fine-mapping with SuSiE model #

Path(s) to fine-mapping with SuSiE RSS model #

Path(s) to colocalization with SuSiE-coloc #

Links to QTL analysis notebooks #

Please list the links to analysis notebooks in the order you executed our pipeline:

Genotype processing: https://github.com/cumc/fungen-xqtl-analysis/tree/main/analysis/Bush_CWRU/magenta_aa_eqtl_genotype_processing.ipynb
Phenotype processing: https://github.com/cumc/fungen-xqtl-analysis/tree/main/analysis/Bush_CWRU/magenta_aa_eqtl_phenotype_processing.ipynb
Covariate processing: https://github.com/cumc/fungen-xqtl-analysis/tree/main/analysis/Bush_CWRU/magenta_aa_eqtl_covariate_processing.ipynb
TensorQTL analysis: https://github.com/cumc/fungen-xqtl-analysis/tree/main/analysis/Bush_CWRU/magenta_aa_eqtl_tensorqtl.ipynb
Complete analysis pipeline: https://github.com/cumc/fungen-xqtl-analysis/tree/main/analysis/Bush_CWRU/magenta_aa_eqtl_complete_analysis.ipynb