Last updated: 2018-10-29

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Unstaged changes:
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    Modified:   analysis/39indQC.Rmd
    Modified:   analysis/characterizeNuclearApaQtls.Rmd
    Modified:   analysis/cleanupdtseq.internalpriming.Rmd
    Modified:   analysis/coloc_apaQTLs_protQTLs.Rmd
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    Modified:   analysis/diff_iso_pipeline.Rmd
    Modified:   analysis/explore.filters.Rmd
    Modified:   analysis/overlapMolQTL.Rmd
    Modified:   analysis/overlap_qtls.Rmd
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    File Version Author Date Message
    Rmd 42d0e3d Briana Mittleman 2018-10-29 add gwas overlap to index

In this analysis I want to see if APAqtls show up in the GWAS catelog. I then want to see if they explain different signal then overlappnig the eQTLs.

I can use my significant snp bed file from /project2/gilad/briana/threeprimeseq/data/perm_APAqtl_trans/sigSnps to overlap with the GWAS catelog. First I can look at direct location then I will use an LD cutoff to colocalize.

  • /project2/gilad/briana/threeprimeseq/data/perm_APAqtl_trans/sigSnps/ApaQTLsignificantSnps_10percFDR_Nuclear.sort.bed
  • /project2/gilad/briana/threeprimeseq/data/perm_APAqtl_trans/sigSnps/ApaQTLsignificantSnps_10percFDR_Total.sort.bed

The downloaded GWAS catalog from the UCSD table browser.

  • /project2/gilad/briana/genome_anotation_data/hg19GwasCatalog.txt

I will make this into a bed format to use with pybedtools.

-Chrom -start -end -name -score

fin=open("/project2/gilad/briana/genome_anotation_data/hg19GwasCatalog.txt", "r")
fout=open("/project2/gilad/briana/genome_anotation_data/hg19GwasCatalog.bed","w")

for num, ln in enumerate(fin):
  if num > 0: 
    line=ln.split("\t")
    id_list=[line[4],line[5], line[14]]
    start=int(line[2])
    end=int(line[3])
    id=":".join(id_list)
    chr=line[1][3:]
    pval=line[16]
    fout.write("%s\t%d\t%d\t%s\t%s\n"%(chr,start, end, id, pval)
fout.close()

Pybedtools to intersect my snps with catelog /project2/gilad/briana/threeprimeseq/data/GWAS_overlap

output dir:

import pybedtools
gwas=pybedtools.BedTool("/project2/gilad/briana/genome_anotation_data/hg19GwasCatalog.sort.bed")
nuc=pybedtools.BedTool("/project2/gilad/briana/threeprimeseq/data/perm_APAqtl_trans/sigSnps/ApaQTLsignificantSnps_10percFDR_Nuclear.sort.bed")
tot=pybedtools.BedTool("/project2/gilad/briana/threeprimeseq/data/perm_APAqtl_trans/sigSnps/ApaQTLsignificantSnps_10percFDR_Total.sort.bed") 

nucOverGWAS=nuc.intersect(gwas, wa=True,wb=True)
totOverGWAS=tot.intersect(gwas,wa=True, wb=True)

#this only results in one overlap:  
nucOverGWAS.saveas("/project2/gilad/briana/threeprimeseq/data/GWAS_overlap/nucFDR10overlapGWAS.txt")

Problem: I see this snp but it is assoicated with a different gene. I need to think about gene and snp overlap.

I can see if this snp is an eqtl.

16:30482494

eqtl=read.table(file = "../data/other_qtls/fastqtl_qqnorm_RNAseq_phase2.fixed.perm.out")
eqtl_g= read.table("../data/other_qtls/fastqtl_qqnorm_RNAseqGeuvadis.fixed.perm.out")

This snp is not in either of these files. I will check for them in the nominal results.

grep 16:30482494   /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_RNAseq_phase2.fixed.nominal.out


grep 16:30482494   /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_RNAseqGeuvadis.fixed.nominal.out

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_0.12.19      digest_0.6.17    
 [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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