ROSMAP DLPFC alternative splicing QTL · FunGen-xQTL Resources

Where	ID	Access	What you get
Synapse	syn69670592	Controlled	Results described below

Contact

Shrishtee Kandoi and Xuanhe Chen (xuanhechenxhc@163.com)

Study Overview

Study name : ROSMAP DLPFC sQTL
Study Description : Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) sQTL analysis summary statistics using the FGC xQTL pipeline.

Samples’ phenotype information (sex, age, race etc.) can be found in ROSMAP metadata, see “Other information” section in this document

Analysis Status

TransQTL association: Need to be performed.

Analysis Details

Sample size tracking through the analysis workflow

Step	Sample Size
Raw data	1141
After overlapping with ROSMAP WGS	839

QC and Normalization Details for Phenotype Data

In the case of leafcutter data, any features with over 40% missing values across samples were removed. The remaining missing values were replaced with the mean of existing values, and introns with less than 0.005 variation were eliminated. A scaled normalization was performed on each intron cluster (representing a row of leafcutter data), followed by Quantile-Quantile Normalization on each sample (representing a column of leafcutter data). In contrast, psichomics phenotype data underwent a different imputation approach; zero-imputation was performed to retain “no event detected” information, and only scaled normalization was applied to each event (row).

Genotype parameters

Kinship coefficient for related individuals: 0.0625
Minor allele count cutoff for single variant analysis: 5
Variant level missingness threshold: 0.1
Sample level missingness threshold: 0.1
HWE filter: 1e-06

Covariate parameters

PCA analysis:

MAF for PCA: 0.01
LD pruning via PLINK for PCA analysis: window 50, shift 10, r2 0.1
Tolerance of missingness in covariates: 0.3
number of pc that captured more than 70% PVE were kept

PEER analysis (Default values from PEER software):

The number of max iteration: 1000
Prior parameter Alpha_a: 0.001
Prior parameter Alpha_b: 0.1
Prior parameter Eps_a: 0.1
Prior parameter Eps_b: 10.0
Tolerance parameter tol: 0.001
Tolerance parameter var_tol: 0.00001
minimum variance explained criteria to drop factors while training r2_tol: False
Convergence mode: “fast”

Final covariates: Sex, Age at death, PMI, PCs(13), PEER factors(60)

TensorQTL association scan parameters

cis window for the up and downstream radius to analyze around the region of interest, in units of bp: 1000000
Minor allele count cutoff: 5
Minor allele frequency cutoff: 5/(2N), where N is the number of samples in the analysis. The pipeline computes N from the covariate file, so the cutoff differs between datasets.

Links to QTL analysis notebooks for LeafCutter2

See notebooks in:

https://github.com/cumc/xqtl-analysis/tree/main/analysis/Wang_Columbia/ROSMAP/sQTL/DLPFC

The notebooks in this folder contain the commands and data wrangling codes for analysis of the eQTL and sQTL data in ROSMAP. (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). Since the sQTL phenotype pre-processing used eQTL STAR alignment output, some of the early stage code are shared.

Association data preprocessing

LeafCutter2_QC shows the commands used for quality control of the LeafCutter2 results.
genotype_preprocessing.ipynb shows the commands used for genotype processing and preparation steps.all QTLs in one cohort have the same genotype_preprocessing procedure.
phenotype_preprocessing.ipynb shows the commands used for the phenotype data processing and preparation steps.
covariate_preprocessing.ipynb shows the commands used for the covariate data processing and preparation steps.

Association scan using TensorQTL and summary statistics standardization

TensorQTL.ipynb provides the pipeline to generate TensorQTL cis association results for all QTLs.
ROSMAP_sQTL_LeafCutter2_commands provides information about the input files for AC/DLPFC/PCC TensorQTL cis association in the base_params variable in [generate_command_1].

SuSiE univariate fine mapping

fine_mapping.ipynb contains the workflow of sQTL univariate fine mapping using filterd psichomics data.

Dataset Details

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

Path(s) to genotype matrix

output of genotype_qc.ipynb

Path(s) to omics-data matrix

output of phenotype_preprocessing_sqtl.ipynb

leafCutter:

psichomics:

text
$ ls -lh *.{txt,bed}
-rw-r--r-- 1 xc2610 xc2610 2.7K Apr  3 14:41 ROSMAP_psichomics_bed_recipe.txt
-rw-r--r-- 1 xc2610 xc2610  65M Apr 14 17:00 ROSMAP.psichomics.qqnorm.revised.formated_chr10.bed
-rw-r--r-- 1 xc2610 xc2610 113M Apr 14 17:00 ROSMAP.psichomics.qqnorm.revised.formated_chr11.bed
-rw-r--r-- 1 xc2610 xc2610 102M Apr 14 17:00 ROSMAP.psichomics.qqnorm.revised.formated_chr12.bed
-rw-r--r-- 1 xc2610 xc2610  28M Apr 14 17:01 ROSMAP.psichomics.qqnorm.revised.formated_chr13.bed
-rw-r--r-- 1 xc2610 xc2610  69M Apr 14 17:01 ROSMAP.psichomics.qqnorm.revised.formated_chr14.bed
-rw-r--r-- 1 xc2610 xc2610  58M Apr 14 17:01 ROSMAP.psichomics.qqnorm.revised.formated_chr15.bed
-rw-r--r-- 1 xc2610 xc2610  88M Apr 14 17:01 ROSMAP.psichomics.qqnorm.revised.formated_chr16.bed
-rw-r--r-- 1 xc2610 xc2610 125M Apr 14 17:01 ROSMAP.psichomics.qqnorm.revised.formated_chr17.bed
-rw-r--r-- 1 xc2610 xc2610  26M Apr 14 17:01 ROSMAP.psichomics.qqnorm.revised.formated_chr18.bed
-rw-r--r-- 1 xc2610 xc2610 117M Apr 14 17:01 ROSMAP.psichomics.qqnorm.revised.formated_chr19.bed
-rw-r--r-- 1 xc2610 xc2610 166M Apr  5 14:34 ROSMAP.psichomics.qqnorm.revised.formated_chr1.bed
-rw-r--r-- 1 xc2610 xc2610  52M Apr 14 17:01 ROSMAP.psichomics.qqnorm.revised.formated_chr20.bed
-rw-r--r-- 1 xc2610 xc2610  18M Apr 14 17:01 ROSMAP.psichomics.qqnorm.revised.formated_chr21.bed
-rw-r--r-- 1 xc2610 xc2610  50M Apr 14 17:01 ROSMAP.psichomics.qqnorm.revised.formated_chr22.bed
-rw-r--r-- 1 xc2610 xc2610 122M Apr  5 16:55 ROSMAP.psichomics.qqnorm.revised.formated_chr2.bed
-rw-r--r-- 1 xc2610 xc2610 108M Apr 14 17:00 ROSMAP.psichomics.qqnorm.revised.formated_chr3.bed
-rw-r--r-- 1 xc2610 xc2610  60M Apr 14 17:00 ROSMAP.psichomics.qqnorm.revised.formated_chr4.bed
-rw-r--r-- 1 xc2610 xc2610  75M Apr 14 17:00 ROSMAP.psichomics.qqnorm.revised.formated_chr5.bed
-rw-r--r-- 1 xc2610 xc2610  80M Apr 14 17:00 ROSMAP.psichomics.qqnorm.revised.formated_chr6.bed
-rw-r--r-- 1 xc2610 xc2610  84M Apr 14 17:00 ROSMAP.psichomics.qqnorm.revised.formated_chr7.bed
-rw-r--r-- 1 xc2610 xc2610  62M Apr 14 17:00 ROSMAP.psichomics.qqnorm.revised.formated_chr8.bed
-rw-r--r-- 1 xc2610 xc2610  66M Apr 14 17:00 ROSMAP.psichomics.qqnorm.revised.formated_chr9.bed
-rw-r--r-- 1 xc2610 xc2610 426K Feb 13 01:15 ROSMAP.psichomics.qqnorm.revised.formated_chrMT.bed
-rw-r--r-- 1 xc2610 xc2610  47M Feb 13 01:15 ROSMAP.psichomics.qqnorm.revised.formated_chrX.bed
-rw-r--r-- 1 xc2610 xc2610 529K Feb 13 01:15 ROSMAP.psichomics.qqnorm.revised.formated_chrY.bed

Path(s) to covariate data matrix

output of covariate_preprocessing.ipynb

leafCutter:

psichomics:

text

$ ls -lh *.gz
-rw-r--r-- 1 xc2610 xc2610 546K Feb  9 13:06 psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.gz

Path(s) to QTL results

output of association_scan_sQTL.ipynb

leafCutter:

psichomics:

text
$ls -lh *.txt
-rw-r--r-- 1 xc2610 xc2610 928K Feb 13 02:34 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.10.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 7.4G Feb 13 01:45 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.10.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 1.6M Feb 13 03:08 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.11.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610  12G Feb 13 01:51 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.11.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 1.5M Feb 13 03:26 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.12.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610  11G Feb 13 01:53 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.12.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 389K Feb 13 02:57 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.13.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 3.2G Feb 13 02:36 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.13.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 973K Feb 13 03:35 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.14.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 7.9G Feb 13 02:44 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.14.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 813K Feb 13 03:24 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.15.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 5.7G Feb 13 02:46 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.15.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 1.2M Feb 13 03:53 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.16.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 9.8G Feb 13 02:50 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.16.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 1.8M Feb 13 04:39 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.17.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610  14G Feb 13 03:01 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.17.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 353K Feb 13 03:18 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.18.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 2.8G Feb 13 03:01 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.18.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 1.6M Feb 13 05:01 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.19.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610  16G Feb 13 03:25 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.19.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 2.3M Feb 13 04:16 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.1.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610  17G Feb 13 02:03 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.1.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 729K Feb 13 03:36 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.20.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 5.7G Feb 13 03:00 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.20.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 254K Feb 13 03:25 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.21.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 2.1G Feb 13 03:12 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.21.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 712K Feb 13 03:58 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.22.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 5.9G Feb 13 03:19 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.22.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 1.7M Feb 13 03:16 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.2.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610  13G Feb 13 01:53 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.2.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 1.5M Feb 13 03:11 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.3.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610  11G Feb 13 01:51 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.3.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 839K Feb 13 02:30 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.4.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 6.7G Feb 13 01:44 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.4.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 1.1M Feb 13 02:37 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.5.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 7.9G Feb 13 01:45 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.5.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 1.1M Feb 13 03:02 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.6.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610  12G Feb 13 01:51 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.6.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 1.2M Feb 13 02:51 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.7.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 9.5G Feb 13 01:49 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.7.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 871K Feb 13 02:31 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.8.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 6.8G Feb 13 01:45 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.8.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 939K Feb 13 02:39 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.9.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 7.5G Feb 13 01:46 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.9.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610  27M Feb 13 05:02 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.emprical.cis_sumstats.txt

psichomics (grouped by each gene - event_type pair):

text
$ ls -lh *.txt
-rw-r--r-- 1 xc2610 xc2610 229K Apr  3 15:30 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.10.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 1.8G Apr  3 14:49 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.10.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 414K Apr  3 15:53 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.11.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 2.9G Apr  3 14:52 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.11.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 373K Apr  3 16:12 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.12.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 2.7G Apr  3 15:10 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.12.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610  99K Apr  3 15:46 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.13.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 785M Apr  3 15:29 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.13.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 249K Apr  3 16:16 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.14.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 2.0G Apr  3 15:33 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.14.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 213K Apr  3 16:18 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.15.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 1.5G Apr  3 15:47 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.15.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 332K Apr  3 16:30 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.16.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 2.6G Apr  3 15:38 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.16.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 453K Apr  3 17:19 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.17.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 3.4G Apr  3 16:01 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.17.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610  91K Apr  3 16:04 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.18.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 699M Apr  3 15:49 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.18.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 471K Apr  3 17:18 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.19.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 4.3G Apr  3 15:55 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.19.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 617K Apr  3 16:33 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.1.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 4.3G Apr  3 14:55 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.1.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 182K Apr  3 16:05 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.20.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 1.4G Apr  3 15:34 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.20.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610  73K Apr  3 16:06 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.21.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 577M Apr  3 15:55 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.21.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 194K Apr  3 16:30 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.22.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 1.6G Apr  3 15:58 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.22.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 434K Apr  3 16:01 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.2.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 3.1G Apr  3 14:52 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.2.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 394K Apr  3 15:53 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.3.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 2.7G Apr  3 14:51 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.3.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 220K Apr  3 15:25 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.4.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 1.7G Apr  3 14:48 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.4.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 286K Apr  3 15:42 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.5.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 2.1G Apr  3 14:50 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.5.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 319K Apr  3 15:52 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.6.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 3.4G Apr  3 14:51 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.6.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 331K Apr  3 15:43 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.7.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 2.6G Apr  3 14:50 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.7.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 234K Apr  3 15:26 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.8.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 1.8G Apr  3 14:48 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.8.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 243K Apr  3 15:29 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.9.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 1.9G Apr  3 14:49 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.9.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 7.4M Apr  3 17:21 ROSMAP_psichomics_bed_recipe_psichomics.dlpfc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.emprical.cis_sumstats.txt

Path(s) to fine-mapping with SuSiE model

output of fine_mapping.ipynb

The results are seperated in psi_A3SS, psi_A5SS, psi_AFE, psi_ALE, psi_MXE, psi_SE sub directories according to their event type. Due to the massive amount of files for splicing data they are not listed here.

Path(s) to cis-QTL association testing

output of TensorQTL.ipynb

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

Fine-mapping model objects (SuSiE-RSS, .rds) are available in the finemapping models folder (syn69670592).

Path(s) to TWAS models

Pre-trained TWAS weight models for this context: syn69670600

Quantile TWAS (qTWAS) models: syn69670611

Path(s) to colocalization with SuSiE-coloc / ColocBoost

Multi-context colocalization models (ColocBoost): syn69670597

AD GWAS–xQTL colocalization results: syn69865816

AD GWAS–xQTL colocalization models: syn69670630

Access

Contact

Study Overview

Analysis Status

Analysis Details

Sample size tracking through the analysis workflow

QC and Normalization Details for Phenotype Data

Genotype parameters

Covariate parameters

TensorQTL association scan parameters

Links to QTL analysis notebooks for LeafCutter2

Association data preprocessing

Association scan using TensorQTL and summary statistics standardization

SuSiE univariate fine mapping

Dataset Details

Path(s) to genotype matrix

Path(s) to omics-data matrix

Path(s) to covariate data matrix

Path(s) to QTL results

Path(s) to fine-mapping with SuSiE model

Path(s) to cis-QTL association testing

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

Path(s) to TWAS models

Path(s) to colocalization with SuSiE-coloc / ColocBoost

Related datasets