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osteo_enrichment.sh
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#!/bin/bash
PROJECT=chengcancer
echo "PROJECT=${PROJECT}"
#JOBNAME=`(basename $0) | sed -e 's/\.[^.]*$//'` #tophat_mapping_y
JOBNAME='enrich'
echo "JOBNAME=${JOBNAME}"
NCORE_REQ=2 #based on Charlie's benmark, the increased number of cores above 4 didn't play much in performance gain for tophat,user can experiment this more to set the best value
echo "NCORE_REQ=${NCORE_REQ}"
RT_LIMIT="48:00:00"
MEM_LIMIT="125G" # it seems each job do not consume 10G to my observation; so set 125G shall be safe, even after increase the cores.
#FILE_COUNT=`find /restricted/projectnb/chengcancer/Simon/project/T2D/bulk_RNA-seq/merge_170415_NB501164_170506_NB501164/2mapping/QT/GTeX_bagged_eQTL/* -maxdepth 0 -type d | wc -l`
#echo "FILE_COUNT=${FILE_COUNT}"
# Let each directory of GTeX bagged eQTL be processed by various p-value cut-off bins
cd /restricted/projectnb/chengcancer/Simon/project/T2D/bulk_RNA-seq/merge_170415_NB501164_170506_NB501164/2mapping/QT/osteoblast/smallest_pval_data/osteo_bagged
#for GTeX in /restricted/projectnb/chengcancer/Simon/project/T2D/bulk_RNA-seq/merge_170415_NB501164_170506_NB501164/2mapping/QT/GTeX_bagged_eQTL/*/ ;
#do
# mkdir $(basename ${file} _Analysis_chrpos_pval.txt.gz)
#GTeX=${GTeX%*/}
GTeX="/restricted/projectnb/chengcancer/Simon/project/T2D/bulk_RNA-seq/merge_170415_NB501164_170506_NB501164/2mapping/QT/osteoblast/smallest_pval_data/osteo_bagged"
echo ${GTeX##*/}
# The GWAS here is actually bone eQTL
GWAS="/restricted//projectnb//chengcancer//Simon//project//T2D//bulk_RNA-seq//merge_170415_NB501164_170506_NB501164//2mapping//QT//eQTL"
# make one enrichment analysis with open cut-off
GTeX_eQTLpvalueUpperBound=1e-2
GTeX_eQTLpvalueLowerBound=1e-100
sigGWASpvalueCutoff=1e-4
echo ${GTeX_eQTLpvalueUpperBound}
echo ${GTeX_eQTLpvalueLowerBound}
outputFilePath="/restricted/projectnb/chengcancer/Simon/project/T2D/bulk_RNA-seq/merge_170415_NB501164_170506_NB501164/2mapping/QT/osteoblast/smallest_pval_data/"
qsub -P $PROJECT -N $JOBNAME -pe omp $NCORE_REQ -l mem_total=${MEM_LIMIT} -l h_rt=${RT_LIMIT} -v eQTLfilePath=${GTeX} -v GWASfilePath=${GWAS} -v GTeX_eQTLpvalueUpperBound=${GTeX_eQTLpvalueUpperBound} -v GTeX_eQTLpvalueLowerBound=${GTeX_eQTLpvalueLowerBound} -v sigGWASpvalueCutoff=${sigGWASpvalueCutoff} -v outdir=${outputFilePath} /restricted/projectnb/chengcancer/Simon/project/T2D/bulk_RNA-seq/merge_170415_NB501164_170506_NB501164/2mapping/QT/osteoblast/smallest_pval_data/osteo_enrichment.qsub
for power in {2..10..2};
do
pow2=$[${power}+2]
GTeX_eQTLpvalueUpperBound=1e-${power}
GTeX_eQTLpvalueLowerBound=1e-${pow2}
echo ${GTeX_eQTLpvalueUpperBound}
echo ${GTeX_eQTLpvalueLowerBound}
qsub -P $PROJECT -N $JOBNAME -pe omp $NCORE_REQ -l mem_total=${MEM_LIMIT} -l h_rt=${RT_LIMIT} -v eQTLfilePath=${GTeX} -v GWASfilePath=${GWAS} -v GTeX_eQTLpvalueUpperBound=${GTeX_eQTLpvalueUpperBound} -v GTeX_eQTLpvalueLowerBound=${GTeX_eQTLpvalueLowerBound} -v sigGWASpvalueCutoff=${sigGWASpvalueCutoff} -v outdir=${outputFilePath} /restricted/projectnb/chengcancer/Simon/project/T2D/bulk_RNA-seq/merge_170415_NB501164_170506_NB501164/2mapping/QT/osteoblast/smallest_pval_data/osteo_enrichment.qsub
done