Last updated: 2019-02-18
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Knit directory: threeprimeseq/analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 3c1f049 | Briana Mittleman | 2019-02-18 | add gwas overlap |
In this analysis I will look at the apaQTLs to draw biological insight. To do this I will run the following analysis:
Look at chromatin regions for QTLs (chromHMM)
Overlap apaQTLs between fractions
Overlap apaQTLs with GWAS
I did this analysis with the QTLs in the preprocessed 39 individual analysis. I will follow a similar pipeline here. I will find all of the snps in LD with the QTLs then test for these in the GWAS catelog. The pipeline I used to get the LD for all of the snp is shown here. The plink files are in /project2/gilad/briana/threeprimeseq/data/GWAS_overlap/. There are both map and ped files.
I can now adapt the subset_plink4QTLs.py file to take the current QTLs list. The file just has the QTLs with the chromosome and position. I can make this and put it in:
/project2/gilad/briana/threeprimeseq/data/GWAS_overlap_processed
The 50mb QTLs are in /project2/gilad/briana/threeprimeseq/data/ApaQTLs.
The QTL snps are in the 6th column.
cut -f6 -d" " /project2/gilad/briana/threeprimeseq/data/ApaQTLs/NuclearapaQTLs.GeneLocAnno.noMP.5perc.10FDR.txt | uniq > /project2/gilad/briana/threeprimeseq/data/ApaQTLs/NuclearQTLs_uniq_50mb.txt
cut -f6 -d" " /project2/gilad/briana/threeprimeseq/data/ApaQTLs/TotalapaQTLs.GeneLocAnno.noMP.5perc.10FDR.txt | uniq > /project2/gilad/briana/threeprimeseq/data/ApaQTLs/TotalQTLs_uniq_50mb.txtI can convert these the the way they are in GEU snp files tony made (snp_num_pos)
QTLs2GeuSnps_proc.py
tot_in=open("/project2/gilad/briana/threeprimeseq/data/ApaQTLs/TotalQTLs_uniq_50mb.txt", "r")
nuc_in=open("/project2/gilad/briana/threeprimeseq/data/ApaQTLs/NuclearQTLs_uniq_50mb.txt", "r")
tot_out=open("/project2/gilad/briana/threeprimeseq/data/ApaQTLs/TotalQTLs_uniq_50mb_GEU.txt", "w")
nuc_out=open("/project2/gilad/briana/threeprimeseq/data/ApaQTLs/NuclearQTLs_uniq_50mb_GEU.txt", "w")
def fix_file(fin, fout):
for ln in fin:
chrom, pos = ln.split(":")
fout.write("snp_%s_%s"%(chrom,pos))
fout.close()
fix_file(tot_in, tot_out)
fix_file(nuc_in, nuc_out)subset_plink4QTLs_proc.py
def main(genFile, qtlFile, outFile):
#convert snp file to a list:
def file_to_list(file):
snp_list=[]
for ln in file:
snp=ln.strip()
snp_list.append(snp)
return(snp_list)
gen=open(genFile,"r")
fout=open(outFile, "w")
qtls=open(qtlFile, "r")
qtl_list=file_to_list(qtls)
for ln in gen:
snp=ln.split()[2]
if snp in qtl_list:
fout.write(ln)
fout.close()
if __name__ == "__main__":
import sys
chrom=sys.argv[1]
fraction=sys.argv[2]
genFile = "/project2/gilad/briana/threeprimeseq/data/GWAS_overlap/geu_plinkYRI_LDchr%s.ld"%(chrom)
outFile= "/project2/gilad/briana/threeprimeseq/data/GWAS_overlap_processed/%sApaQTL_LD/chr%s.%sQTL.LD.geno.ld"%(fraction,chrom,fraction)
qtlFile= "/project2/gilad/briana/threeprimeseq/data/ApaQTLs/%sQTLs_uniq_50mb_GEU.txt"%(fraction)
main(genFile, qtlFile, outFile) run_subset_plink4QTLs_proc.sh
#!/bin/bash
#SBATCH --job-name= run_subset_plink4QTLs_proc
#SBATCH --account=pi-yangili1
#SBATCH --time=36:00:00
#SBATCH --output=run_subset_plink4QTLs_proc.out
#SBATCH --error=run_subset_plink4QTLs_proc.err
#SBATCH --partition=broadwl
#SBATCH --mem=30G
#SBATCH --mail-type=END
module load Anaconda3
source activate three-prime-env
for i in {1..22};
do
python subset_plink4QTLs_proc.py ${i} "Total"
done
for i in {1..22};
do
python subset_plink4QTLs_proc.py ${i} "Nuclear"
doneThis added 2446 total snps and 6258 nuclear snps.
Cat and remove indels:
cat chr* > allChr.TotalQTL.LD.gene.ld
grep -v indel allChr.TotalQTL.LD.gene.ld > allChr.TotalQTL.LD.gene.ld_noIndel
cat chr* > allChr.NuclearQTL.LD.gene.ld
grep -v indel allChr.NuclearQTL.LD.gene.ld > allChr.NuclearQTL.LD.gene.ld_noIndelMake these bed files:
makeAlloverlapbed_proc.py
#load files:
QTL_total=open("/project2/gilad/briana/threeprimeseq/data/ApaQTLs/TotalQTLs_uniq_50mb_GEU.txt", "r")
QTL_nuclear=open("/project2/gilad/briana/threeprimeseq/data/ApaQTLs/NuclearQTLs_uniq_50mb_GEU.txt", "r")
LD_total=open("/project2/gilad/briana/threeprimeseq/data/GWAS_overlap_processed/TotalApaQTL_LD/allChr.TotalQTL.LD.gene.ld_noIndel", "r")
LD_nuclear=open("/project2/gilad/briana/threeprimeseq/data/GWAS_overlap_processed/NuclearApaQTL_LD/allChr.NuclearQTL.LD.gene.ld_noIndel", "r")
outFile= open("/project2/gilad/briana/threeprimeseq/data/GWAS_overlap_processed/AllOverlapSnps.bed", "w")
#function for qtl to bed format
def qtl2bed(fqtl, fraction, fout=outFile):
for ln in fqtl:
snp, chrom, pos = ln.split("_")
start=int(pos)-1
end= int(pos)
fout.write("%s\t%d\t%d\tQTL_%s\n"%(chrom, start, end,fraction))
#function for ld to bed format
def ld2bed(fLD, fraction, fout=outFile):
for ln in fLD:
snpID=ln.split()[5]
snp, chrom, pos= snpID.split("_")
start=int(pos)-1
end=int(pos)
fout.write("%s\t%d\t%d\tLD_%s\n"%(chrom, start, end,fraction))
#I will run each of these for both fractions to get all of the snps in the out file.
qtl2bed(QTL_nuclear, "Nuclear")
qtl2bed(QTL_total, "Total")
ld2bed(LD_nuclear, "Nuclear")
ld2bed(LD_total, "Total")
outFile.close()Sort this:
sort -k1,1 -k2,2n /project2/gilad/briana/threeprimeseq/data/GWAS_overlap_processed/AllOverlapSnps.bed > /project2/gilad/briana/threeprimeseq/data/GWAS_overlap_processed/AllOverlapSnps.sort.bedOverlap with GWAS
I can use the overlapSNPsGWAS.py file I created in the previous rendition of this analysis but run it with these files.
run_overlapSNPsGWAS_proc.sh
#!/bin/bash
#SBATCH --job-name=run_overlapSNPsGWAS_proc
#SBATCH --account=pi-yangili1
#SBATCH --time=5:00:00
#SBATCH --output=run_overlapSNPsGWAS_proc.out
#SBATCH --error=run_overlapSNPsGWAS_proc.err
#SBATCH --partition=broadwl
#SBATCH --mem=10G
#SBATCH --mail-type=END
module load Anaconda3
source activate three-prime-env
python overlapSNPsGWAS.py "/project2/gilad/briana/threeprimeseq/data/GWAS_overlap_processed/AllOverlapSnps.sort.bed" "/project2/gilad/briana/threeprimeseq/data/GWAS_overlap_processed/AllSnps_GWASoverlapped.txt"Total QTLs overlap: rs3117582 6:31620520
Total LD overlap:
Nuclear QTL overlap:
rs7206971 17:45425115
Nucelar LD overlapL
Are these eQTLs?
sessionInfo()R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.14.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] workflowr_1.2.0 Rcpp_0.12.19 digest_0.6.17 rprojroot_1.3-2
[5] backports_1.1.2 git2r_0.24.0 magrittr_1.5 evaluate_0.13
[9] stringi_1.2.4 fs_1.2.6 whisker_0.3-2 rmarkdown_1.11
[13] tools_3.5.1 stringr_1.4.0 glue_1.3.0 yaml_2.2.0
[17] compiler_3.5.1 htmltools_0.3.6 knitr_1.20