ROSMAP PCC alternative splicing QTL #
Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) PCC alternative splicing. Please refer to this document for an overview of the ROSMAP project.
Contact #
Frank Grenn
Study Overview #
In progress
- Sample information:
####/####_sample_attributes.csv. - Lab protocol:
####/####_lab_protocol.csv. - Computational protocol:
####/####_computational_protocol.csv. - QTL summary statistics output:
####/####.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.
Analysis Status #
TransQTL association: Need to be performed.
Dataset Details #
Path(s) to genotype matrix #
- Zhang Lab,
/restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/genotype/genotype_partition/ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.plink_files_list.txt
$ head ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.plink_files_list.txt
#id dir
1 /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/genotype/genotype_partition/ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.1.bed
2 /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/genotype/genotype_partition/ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.2.bed
3 /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/genotype/genotype_partition/ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.3.bed
4 /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/genotype/genotype_partition/ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.4.bed
5 /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/genotype/genotype_partition/ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.5.bed
6 /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/genotype/genotype_partition/ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.6.bed
7 /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/genotype/genotype_partition/ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.7.bed
8 /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/genotype/genotype_partition/ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.8.bed
9 /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/genotype/genotype_partition/ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.9.bed
$ ls -lh *.{bim,bed,fam} | head
-rw-r--r-- 1 fgrennjr casa 91M Mar 17 14:03 ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.1.bed
-rw-r--r-- 1 fgrennjr casa 33M Mar 17 14:03 ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.1.bim
-rw-r--r-- 1 fgrennjr casa 8.7K Mar 17 14:03 ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.1.fam
-rw-r--r-- 1 fgrennjr casa 59M Mar 17 14:03 ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.10.bed
-rw-r--r-- 1 fgrennjr casa 23M Mar 17 14:03 ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.10.bim
-rw-r--r-- 1 fgrennjr casa 8.7K Mar 17 14:03 ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.10.fam
-rw-r--r-- 1 fgrennjr casa 57M Mar 17 14:03 ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.11.bed
-rw-r--r-- 1 fgrennjr casa 22M Mar 17 14:03 ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.11.bim
-rw-r--r-- 1 fgrennjr casa 8.7K Mar 17 14:03 ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.11.fam
-rw-r--r-- 1 fgrennjr casa 56M Mar 17 14:03 ROSMAP_NIA_WGS.leftnorm.filtered.unrelated.filtered.12.bed
Path(s) to omics-data matrix #
- Zhang Lab,
/restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/PDP_leafcutter/batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.per_chrom.recipe
$ ls -lh batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.txt
-rw-r--r-- 1 fgrennjr casa 3.1G Mar 6 14:06 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.txt
Path(s) to covariate data matrix #
- Zhang Lab,
/restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/reference_data/ROSMAP_xqtl_covariates_sex_death_pmi_study.tsv
$ head batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.per_chrom.recipe
#id #dir
5 /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/PDP_leafcutter/batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.chr5.bed.gz
18 /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/PDP_leafcutter/batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.chr18.bed.gz
7 /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/PDP_leafcutter/batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.chr7.bed.gz
10 /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/PDP_leafcutter/batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.chr10.bed.gz
8 /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/PDP_leafcutter/batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.chr8.bed.gz
Y /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/PDP_leafcutter/batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.chrY.bed.gz
11 /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/PDP_leafcutter/batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.chr11.bed.gz
13 /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/PDP_leafcutter/batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.chr13.bed.gz
9 /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/PDP_leafcutter/batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.chr9.bed.gz
$ ls -lh *bed.gz | head
-rw-r--r-- 1 fgrennjr casa 125M Mar 8 16:08 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.chr1.bed.gz
-rw-r--r-- 1 fgrennjr casa 56M Mar 8 16:07 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.chr10.bed.gz
-rw-r--r-- 1 fgrennjr casa 67M Mar 8 16:07 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.chr11.bed.gz
-rw-r--r-- 1 fgrennjr casa 69M Mar 8 16:07 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.chr12.bed.gz
-rw-r--r-- 1 fgrennjr casa 26M Mar 8 16:07 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.chr13.bed.gz
-rw-r--r-- 1 fgrennjr casa 43M Mar 8 16:07 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.chr14.bed.gz
-rw-r--r-- 1 fgrennjr casa 50M Mar 8 16:07 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.chr15.bed.gz
-rw-r--r-- 1 fgrennjr casa 58M Mar 8 16:07 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.chr16.bed.gz
-rw-r--r-- 1 fgrennjr casa 74M Mar 8 16:07 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.chr17.bed.gz
-rw-r--r-- 1 fgrennjr casa 22M Mar 8 16:07 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.chr18.bed.gz
Path(s) to QTL results #
- Zhang Lab,
/restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/TensorQTL/sQTL
$ ls -lh | head
total 27G
-rw-r--r-- 1 fgrennjr casa 374M Mar 24 11:42 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.per_chrom_leafcutter.pcc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.1.cis_qtl_pairs.1.parquet
-rw-r--r-- 1 fgrennjr casa 285 Mar 24 22:12 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.per_chrom_leafcutter.pcc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.1.cis_qtl_pairs.1.parquet.stderr
-rw-r--r-- 1 fgrennjr casa 138K Mar 24 22:12 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.per_chrom_leafcutter.pcc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.1.cis_qtl_pairs.1.parquet.stdout
-rw-r--r-- 1 fgrennjr casa 433K Mar 24 22:12 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.per_chrom_leafcutter.pcc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.1.emprical.cis_sumstats.txt
-rw-r--r-- 1 fgrennjr casa 2.2G Mar 24 11:44 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.per_chrom_leafcutter.pcc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.1.norminal.cis_long_table.txt
-rw-r--r-- 1 fgrennjr casa 180M Mar 24 11:28 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.per_chrom_leafcutter.pcc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.10.cis_qtl_pairs.10.parquet
-rw-r--r-- 1 fgrennjr casa 285 Mar 24 16:48 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.per_chrom_leafcutter.pcc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.10.cis_qtl_pairs.10.parquet.stderr
-rw-r--r-- 1 fgrennjr casa 58K Mar 24 16:48 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.per_chrom_leafcutter.pcc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.10.cis_qtl_pairs.10.parquet.stdout
-rw-r--r-- 1 fgrennjr casa 187K Mar 24 16:48 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.per_chrom_leafcutter.pcc_batch_all.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.10.emprical.cis_sumstats.txt
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 #
Analysis notebook generation in progress and will be uploaded to https://github.com/cumc/fungen-xqtl-analysis/tree/main/analysis/Zhang_BU/PCC_AC. Steps will be similar to what is found in https://github.com/cumc/fungen-xqtl-analysis/tree/main/analysis/Zhang_BU/ROSMAP_DLPFC.