Call aditional molecular QTLs

Last updated: 2018-09-27

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Unstaged changes:
    Modified:   analysis/28ind.peak.explore.Rmd
    Modified:   analysis/cleanupdtseq.internalpriming.Rmd
    Modified:   analysis/dif.iso.usage.leafcutter.Rmd
    Modified:   analysis/diff_iso_pipeline.Rmd
    Modified:   analysis/explore.filters.Rmd
    Modified:   analysis/overlap_qtls.Rmd
    Modified:   analysis/peakOverlap_oppstrand.Rmd
    Modified:   analysis/pheno.leaf.comb.Rmd
    Modified:   analysis/test.max2.Rmd
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File	Version	Author	Date	Message
Rmd	946b744	Briana Mittleman	2018-09-27	add code for prot and RNA
html	47cd4bf	Briana Mittleman	2018-09-26	Build site.
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:

export PATH=/project/gilad/software/midway1/qtltools-1.0:$PATH

RiboQTL

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

I can process these to by generalizing my script from the apaQTLsAllInd.Rmd

Eqtl

I need to remove the Chr and add the NA.

fastqtl_qqnorm_RNAseq_phase2.txt

python addNAphenohead.py /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.txt /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.txt

sed 's/^chr//'  /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.txt > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.txt

bgzip /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.txt
tabix /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.txt.gz


#midway1 
QTLtools pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.txt.gz --scale --center --out /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.PC.txt

#keep top 5 PCs for analysis
head -n 6 fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.PC.txt.pca > fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.5PC.txt.pca 

less fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.5PC.txt.pca | tr " " "\t" > fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.5PC_tab.txt.pca

I want to create a script that checks the samples in the file and then makes a samples.txt file if they are in the VCF.

First create a file with the names of the individuals in the vcf files. /project2/gilad/briana/YRI_geno_hg19/vcf.samples.txt

create_molQTLSamplefile.py


#infile is the pheno PCA file (because it is not zipped)
#outfile is the samples for that pheno if they are in the vcf samples
def main(inF, outF):
    vcf_samp=open("/project2/gilad/briana/YRI_geno_hg19/vcf.samples.txt", "r")
    for line in vcf_samp:
        vcf_list=line.split()
    infile= open(inF, "r")
    fout = open(outF,'w')
    for i, line in enumerate(infile):
        if i ==0: 
            mol_samples=line.split()[1:]
            final_samps=[]
            for i in mol_samples:
                if i in vcf_list:
                    final_samps.append(i)
            fout.write("\n".join(final_samps))


if __name__ == "__main__":
    import sys
    inF = sys.argv[1]
    outF= sys.argv[2]
    main(inF, outF)

Run in the code dir:

python create_molQTLSamplefile.py ../data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.5PC_tab.txt.pca ../data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.Samples.txt

rnaQTL.nom.sh

#!/bin/bash


#SBATCH --job-name=rnaQTL.nom
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=rnaQTL.nom.out
#SBATCH --error=rnaQTL.nom.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END

for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz  --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.5PC_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.txt.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_RNAseq_phase2.fixed.nominal.chunk$i.out --chunk $i 30  --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.Samples.txt
done

rnaQTL.perm.sh

#!/bin/bash


#SBATCH --job-name=rnaQTL.perm
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=rnaQTL.perm.out
#SBATCH --error=rnaQTL.perm.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END

for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --permute 1000 --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz  --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.5PC_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.txt.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/perm/fastqtl_qqnorm_RNAseq_phase2.fixed.perm.chunk$i.out --chunk $i 30  --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.Samples.txt
done

ProteinQTL

http://eqtl.uchicago.edu/jointLCL/fastqtl_qqnorm_prot.txt.gz

python /project2/gilad/briana/threeprimeseq/code/addNAphenohead.py /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.txt /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.txt

sed 's/^chr//'  /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.txt > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.txt

bgzip /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.txt
tabix -p bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.txt.gz


#midway1 
QTLtools pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.txt.gz --scale --center --out /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.PC.txt

#keep top 5 PCs for analysis
head -n 6 /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.PC.txt.pca > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.5PC.txt.pca


less /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.5PC.txt.pca | tr " " "\t" > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.5PC_tab.txt.pca

python create_molQTLSamplefile.py /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.5PC_tab.txt.pca /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.SAMP.txt

protQTL.nom.sh

#!/bin/bash


#SBATCH --job-name=protQTL.nom
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=protQTL.nom.out
#SBATCH --error=protQTL.nom.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END

for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz  --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.5PC_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.txt.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_prot.fixed.nominal.chunk$i.out --chunk $i 30  --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.SAMP.txt
done

protQTL.perm.sh

#!/bin/bash


#SBATCH --job-name=protQTL.perm
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=protQTL.perm.out
#SBATCH --error=protQTL.perm.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END

for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --permute 1000  --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz  --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.5PC_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.txt.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/perm/fastqtl_qqnorm_prot.fixed.nominal.chunk$i.out --chunk $i 30  --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.SAMP.txt
done

Session information

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

This reproducible R Markdown analysis was created with workflowr 1.1.1

Call aditional molecular QTLs

Briana Mittleman

9/25/2018

RiboQTL

Eqtl

ProteinQTL

Session information