rmbedheader.pbs

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

#Request x number of hours of walltime
#PBS -l walltime=08:00:00

#Request 7 gigabyte of memory per process
#PBS -l mem=15gb

#Request that regular output and terminal output go to the same file
#PBS -j oe
#PBS -m abe

date
cd /mnt/nfs/arginine/data1/resAndStdt/transRegVar/exrna/bedgraphs


module load BEDTools

# sed '1d' unionbedg/ERCC.cov.bed > unionbedg/ERCC.cov.noheader.bed
# sort -k1,1 -k2,2n unionbedg/ERCC.cov.noheader.bed > unionbedg/ERCC.cov.noheader.sort.bed

# bedtools merge -i unionbedg/ERCC.cov.noheader.sort.bed > unionbedg/ERCC.cov.noheader.pbs.bed

# cat ASAS.PMID33452016.bed unionbedg/ERCC.cov.noheader.merged.bed > unionbedg/regionsNeeded.bed

# sort -k1,1 -k2,2n unionbedg/regionsNeeded.bed > unionbedg/regionsNeeded.sorted.bed

awk 'BEGIN{FS="\t";OFS="\t"} {print $1,$2,$3,T}' unionbedg/regionsNeeded.sorted.bed > unionbedg/regionsNeeded.sorted.3col.bed

bedtools merge -i unionbedg/regionsNeeded.sorted.3col.bed > unionbedg/regionsNeeded.sorted.merged.bed

date