Last updated: 2018-09-26
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File | Version | Author | Date | Message |
---|---|---|---|---|
Rmd | fa7f707 | Briana Mittleman | 2018-09-26 | ribo QTL code |
I will use this analysis file to recall the other molecular QTLs using the same VCF files I am using for the APAqtls. This is important because we want to overlap QTLs called with the same genotype information.
processed (WASP+normalized) 4sU-seq (30m)
processed (WASP+normalized) 4sU-seq (60m)
processed (WASP+normalized) RNA-seq (Pickrell)
processed (WASP+normalized) RNA-seq (GEUVADIS)
processed (WASP+normalized) ribo-seq
LiftOver from (Battle et al., 2015) protein
I am download the processed data from http://eqtl.uchicago.edu/jointLCL/ and putting it in /project2/gilad/briana/threeprimeseq/data/molecular_phenos.
The protein file is already in the format needed for fastQTL. I need to change the headers to include the NA before the individuals.I will need to use:
bgzip phenotypes.bed && tabix -p bed phenotypes.bed.gz
To index the file for the program.
I will create a python script that adds the NA to the individuals.
def main(inF, outF):
infile= open(inF, "r")
fout = open(outF,'w')
for i, line in enumerate(infile):
if i == 0:
linelist=line.split()
for i, item in enumerate(linelist):
if i > 3:
linelist[i]="NA" + item
fout.write(" ".join(linelist) + '\n' )
else:
fout.write(line)
fout.close()
if __name__ == "__main__":
import sys
inF = sys.argv[1]
outF= sys.argv[2]
main(inF, outF)
Next step is to get the PCs to use as covariates in the analysis.
https://qtltools.github.io/qtltools/
This package is in /project/gilad/software/midway1/ and was installed by Peter Carbaneto from the RCC. I can add this to my path with:
export PATH=/project/gilad/software/midway1/qtltools-1.0:$PATH
I am going to use the QTLtools pca function. I need to run this on midway1.
QTLtools pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_ribo_phase2.fixed.bed.gz --scale --center --out /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_ribo_phase2.fixed.bed.PC.txt
#keep top 5 PCs for analysis
head -n 6 fastqtl_qqnorm_ribo_phase2.fixed.bed.PC.txt.pca > fastqtl_qqnorm_ribo_phase2.fixed.bed.5PCs.txt.pca
I then make a samples file wit the head of the PCA file. Remove 19192,19193 from sample file I need to make 1 vcf file with all of the chroms to run this.
riboQTL.nom.sh
#!/bin/bash
#SBATCH --job-name=riboQTL.nom
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=riboQTL.nom.out
#SBATCH --error=riboQTL.nom.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END
for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_ribo_phase2.fixed.bed.5PCs_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_ribo_phase2.fixed.noChr.bed.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_ribo_phase2.fixed.nominal.out --chunk $i 30 --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/samples.txt
done
problem chr in pheno file and not in vcf
sed 's/^chr//' fastqtl_qqnorm_ribo_phase2.fixed.bed > fastqtl_qqnorm_ribo_phase2.fixed.noChr.bed
try changing /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_ribo_phase2.fixed.bed.5PCs.txt.pca first part of header to id like in the FastQTL site. and use tr to make it tap deliminated from " "
riboQTL.perm.sh
#!/bin/bash
#SBATCH --job-name=riboQTL.perm
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=riboQTL.perm.out
#SBATCH --error=riboQTL.perm.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END
for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --permute 1000 --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_ribo_phase2.fixed.bed.5PCs_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_ribo_phase2.fixed.noChr.bed.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/perm/fastqtl_qqnorm_ribo_phase2.fixed.perm.chunk$i.out --chunk $i 30 --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/samples.txt
done
sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6
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_1.1.1 Rcpp_0.12.18 digest_0.6.16
[4] rprojroot_1.3-2 R.methodsS3_1.7.1 backports_1.1.2
[7] git2r_0.23.0 magrittr_1.5 evaluate_0.11
[10] stringi_1.2.4 whisker_0.3-2 R.oo_1.22.0
[13] R.utils_2.7.0 rmarkdown_1.10 tools_3.5.1
[16] stringr_1.3.1 yaml_2.2.0 compiler_3.5.1
[19] htmltools_0.3.6 knitr_1.20
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