APAqtls with Leafcutter

Last updated: 2018-08-20

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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:  data/18486.genecov.txt
    Untracked:  data/APApeaksYL.total.inbrain.bed
    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/combined_reads_mapped_three_prime_seq.csv
    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/nuc6up/
    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/cleanupdtseq.internalpriming.Rmd
    Modified:   analysis/dif.iso.usage.leafcutter.Rmd
    Modified:   analysis/explore.filters.Rmd
    Modified:   analysis/peak.cov.pipeline.Rmd
    Modified:   analysis/pheno.leaf.comb.Rmd
    Modified:   analysis/test.max2.Rmd
    Modified:   code/Snakefile

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File	Version	Author	Date	Message
Rmd	6b1b51c	brimittleman	2018-08-20	start qtl analsis, add to index

I need to run fastQTL to call the apaQTLs.

Imputed snp: /project2/yangili1/tonyzeng/genotyping/imputation_results/ `

module load samtools
#zip file 
gzip filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Total.txt 

module load python
#leafcutter script
python /project2/gilad/briana/threeprimeseq/code/prepare_phenotype_table.py filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Total.txt.gz 

#source activate three-prime-env
sh filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Total.txt.gz_prepare.sh

#run for nuclear as well 
gzip filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Nuclear.txt 
#unload anaconda, load python
python /project2/gilad/briana/threeprimeseq/code/prepare_phenotype_table.py filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Nuclear.txt.gz 
#load anaconda and env. 
sh filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Nuclear.txt.gz_prepare.sh

#filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Total.txt.gz.PCs
#filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Nuclear.txt.gz.PCs

makeSamplelist.py

#make a sample list  

fout = file("/project2/gilad/briana/threeprimeseq/data/filt_peak_refGene_cov/SAMPLE.txt",'w')

for ln in open("/project2/gilad/briana/threeprimeseq/data/filt_peak_refGene_cov/file_id_mapping_nuc.txt", "r"):
    bam, sample = ln.split()
    line=sample[:-2]
    fout.write("NA"+line + "\n")
fout.close()

APAqtl_nominal_nuc.sh

#!/bin/bash


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

for i in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --vcf /project2/yangili1/tonyzeng/genotyping/imputation_results/chr$i.dose.vcf.gz --cov /project2/gilad/briana/threeprimeseq/data/filt_peak_refGene_cov/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Nuclear.txt.gz.PCs --bed /project2/gilad/briana/threeprimeseq/data/filt_peak_refGene_cov/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Nuclear.txt.gz.qqnorm_chr$i.gz --out /project2/gilad/briana/threeprimeseq/data/nominal_APAqtl/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Nuclear.txt.gz.qqnorm_chr$i.nominal.out --chunk 1 1  --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/filt_peak_refGene_cov/SAMPLE.txt
done

Remove the non matching ind. from the sample list.

Remove 18500, 19092 and 19193, 18497

Try it on the total ones:

APAqtl_nominal_tot.sh

#!/bin/bash


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

for i in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --vcf /project2/yangili1/tonyzeng/genotyping/imputation_results/chr$i.dose.vcf.gz --cov /project2/gilad/briana/threeprimeseq/data/filt_peak_refGene_cov/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Total.txt.gz.PCs --bed /project2/gilad/briana/threeprimeseq/data/filt_peak_refGene_cov/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Total.txt.gz.qqnorm_chr$i.gz --out /project2/gilad/briana/threeprimeseq/data/nominal_APAqtl/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Total.txt.gz.qqnorm_chr$i.nominal.out --chunk 1 1  --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/filt_peak_refGene_cov/SAMPLE.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_0.6.15    
 [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_2.6.0     rmarkdown_1.10    tools_3.5.1      
[16] stringr_1.3.1     yaml_2.1.19       compiler_3.5.1   
[19] htmltools_0.3.6   knitr_1.20

This reproducible R Markdown analysis was created with workflowr 1.1.1

APAqtls with Leafcutter

Briana Mittleman

8/15/2018

Session information