Last updated: 2018-09-28

workflowr checks: (Click a bullet for more information)

  • ✔ R Markdown file: up-to-date

    Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

  • ✔ Environment: empty

    Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

  • ✔ Seed: set.seed(12345)

    The command set.seed(12345) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

  • ✔ Session information: recorded

    Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

  • ✔ Repository version: bfb5092

    Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

    Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated: 
    
Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    output/.DS_Store

Untracked files:
    Untracked:  analysis/ncbiRefSeq_sm.sort.mRNA.bed
    Untracked:  analysis/snake.config.notes.Rmd
    Untracked:  analysis/verifyBAM.Rmd
    Untracked:  data/18486.genecov.txt
    Untracked:  data/APApeaksYL.total.inbrain.bed
    Untracked:  data/NuclearApaQTLs.txt
    Untracked:  data/RNAkalisto/
    Untracked:  data/TotalApaQTLs.txt
    Untracked:  data/Totalpeaks_filtered_clean.bed
    Untracked:  data/YL-SP-18486-T-combined-genecov.txt
    Untracked:  data/YL-SP-18486-T_S9_R1_001-genecov.txt
    Untracked:  data/bedgraph_peaks/
    Untracked:  data/bin200.5.T.nuccov.bed
    Untracked:  data/bin200.Anuccov.bed
    Untracked:  data/bin200.nuccov.bed
    Untracked:  data/clean_peaks/
    Untracked:  data/comb_map_stats.csv
    Untracked:  data/comb_map_stats.xlsx
    Untracked:  data/comb_map_stats_39ind.csv
    Untracked:  data/combined_reads_mapped_three_prime_seq.csv
    Untracked:  data/filtered_APApeaks_merged_allchrom_refseqTrans.closest2End.bed
    Untracked:  data/filtered_APApeaks_merged_allchrom_refseqTrans.closest2End.noties.bed
    Untracked:  data/first50lines_closest.txt
    Untracked:  data/gencov.test.csv
    Untracked:  data/gencov.test.txt
    Untracked:  data/gencov_zero.test.csv
    Untracked:  data/gencov_zero.test.txt
    Untracked:  data/gene_cov/
    Untracked:  data/joined
    Untracked:  data/leafcutter/
    Untracked:  data/merged_combined_YL-SP-threeprimeseq.bg
    Untracked:  data/nom_QTL/
    Untracked:  data/nom_QTL_opp/
    Untracked:  data/nuc6up/
    Untracked:  data/other_qtls/
    Untracked:  data/peakPerRefSeqGene/
    Untracked:  data/perm_QTL/
    Untracked:  data/perm_QTL_opp/
    Untracked:  data/reads_mapped_three_prime_seq.csv
    Untracked:  data/smash.cov.results.bed
    Untracked:  data/smash.cov.results.csv
    Untracked:  data/smash.cov.results.txt
    Untracked:  data/smash_testregion/
    Untracked:  data/ssFC200.cov.bed
    Untracked:  data/temp.file1
    Untracked:  data/temp.file2
    Untracked:  data/temp.gencov.test.txt
    Untracked:  data/temp.gencov_zero.test.txt
    Untracked:  output/picard/
    Untracked:  output/plots/
    Untracked:  output/qual.fig2.pdf

Unstaged changes:
    Modified:   analysis/28ind.peak.explore.Rmd
    Modified:   analysis/PeakToGeneAssignment.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
    Modified:   code/Snakefile
    Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
Expand here to see past versions:
    File Version Author Date Message
    Rmd bfb5092 Briana Mittleman 2018-09-28 4su30qtl code
    html e8acce6 Briana Mittleman 2018-09-28 Build site.
    Rmd 3914988 Briana Mittleman 2018-09-28 4su60qtl code
    html a6038b1 Briana Mittleman 2018-09-27 Build site.
    Rmd 48be5d3 Briana Mittleman 2018-09-27 add 4su processing
    Rmd 79b6c46 Briana Mittleman 2018-09-27 start to 4su
    html d0019be Briana Mittleman 2018-09-27 Build site.
    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

RNAgQTL

fastqtl_qqnorm_RNAseqGeuvadis_phase2.txt.gz

python addNAphenohead.py /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.txt /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.txt

sed 's/^chr//'  /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.txt > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.txt

bgzip /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.txt
tabix -p bed -f /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.txt.gz


#midway1 
QTLtools pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.txt.gz --scale --center --out /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.PC.txt

#keep top 5 PCs for analysis
head -n 6 /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.PC.txt.pca > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.5PC.txt.pca

less /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.5PC.txt.pca | tr " " "\t" > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.5PC_tab.txt.pca
python create_molQTLSamplefile.py /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.5PC_tab.txt.pca /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.SAMP.txt

RNAgQTL.nuc.sh

#!/bin/bash


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

for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz  --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.5PC_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.txt.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_RNAseqGeuvadis.fixed.nominal.chunk$i.out --chunk $i 30  --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.SAMP.txt
done

RNAgQTL.perm.sh

#!/bin/bash


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

for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --permute 1000  --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz  --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.5PC_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.txt.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/perm/fastqtl_qqnorm_RNAseqGeuvadis.fixed.perm.chunk$i.out --chunk $i 30  --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.SAMP.txt
done

4su 60

python addNAphenohead.py /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.txt /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.txt

sed 's/^chr//'  /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.txt > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.txt

bgzip /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.txt
tabix -p bed -f /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.txt.gz


#midway1 
QTLtools pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.txt.gz --scale --center --out /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.PC.txt

#keep top 5 PCs for analysis
head -n 6 /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.PC.txt.pca > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.5PC.txt.pca

less /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.5PC.txt.pca | tr " " "\t" > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.5PC_tab.txt.pca
python create_molQTLSamplefile.py /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.5PC_tab.txt.pca /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.SAMP.txt

4su60QTL_nom.sh

#!/bin/bash


#SBATCH --job-name=4su60QTL_nom
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=4su60QTL_nom.out
#SBATCH --error=4su60QTL_nom.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END

for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz  --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.5PC_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.txt.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_4su60.fixed.nominal.chunk$i.out --chunk $i 30  --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.SAMP.txt  
done

4su60QTL_perm.sh

#!/bin/bash


#SBATCH --job-name=4su60QTL_perm
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=4su60QTL_perm.out
#SBATCH --error=4su60QTL_perm.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END

for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz  --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.5PC_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.txt.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/perm/fastqtl_qqnorm_4su60.fixed.perm.chunk$i.out --chunk $i 30  --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.SAMP.txt  
done

4su 30

python addNAphenohead.py /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.txt /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.txt

sed 's/^chr//'  /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.txt > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.txt

bgzip /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.txt

tabix -p bed -f /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.txt.gz


#midway1 
QTLtools pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.txt.gz --scale --center --out /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.PC.txt

#keep top 5 PCs for analysis
head -n 6 /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.PC.txt.pca > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.5PC.txt.pca

less /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.5PC.txt.pca | tr " " "\t" > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.5PC_tab.txt.pca
python create_molQTLSamplefile.py /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.5PC_tab.txt.pca /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.SAMP.txt

4su30QTL_nom.sh

#!/bin/bash


#SBATCH --job-name=4su30QTL_nom
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=4su30QTL_nom.out
#SBATCH --error=4su30QTL_nom.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END

for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz  --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.5PC_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.txt.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_4su30.fixed.nominal.chunk$i.out --chunk $i 30  --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.SAMP.txt  
done

4su30QTL_perm.sh

#!/bin/bash


#SBATCH --job-name=4su30QTL_perm
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=4su30QTL_perm.out
#SBATCH --error=4su30QTL_perm.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END

for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz  --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.5PC_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.txt.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/perm/fastqtl_qqnorm_4su30.fixed.perm.chunk$i.out --chunk $i 30  --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.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