all_exRNA_collapse.pbs

# processors on 1 node
#PBS -l nodes=1:ppn=1 

#Request walltime/fastq file ~15 min/sample
#PBS -l walltime=72:00:00

#The larger studies should probably request 40 gb
#PBS -l mem=40gb

#Request that regular output and terminal output go to the same file
#PBS -j oe
#PBS -M Emily.Laplante@bcm.edu
#PBS -m abe

cd /scratch/$PBS_JOBID
module load R/3.5

cp /mnt/brlstor/Vol6_SP/exrna/readCoverage/EmilyTest/study_exRNA_coverage/${study}_intersect.bed.tgz /scratch/$PBS_JOBID
tar -xzvf ${study}_intersect.bed.tgz

Rscript /mnt/brlstor/Vol6_SP/exrna/readCoverage/EmilyTest/collapse_exRNA_coverage.R ${cov}

mv out.txt ${study}_coverage_${cov}.bedgraph
mv ${study}_coverage_${cov}.bedgraph /mnt/brlstor/Vol6_SP/exrna/readCoverage/EmilyTest/study_exRNA_coverage/${study}_coverage_${cov}.bedgraph