prod_reproduction/202307-FeBY2/gc/run_targetBed_ref.pbs

#! /usr/bin/sh
#PBS -N GC
#PBS -j oe
#PBS -l ncpus=8
#PBS -l nodes=1
#PBS -l mem=20G
cd ${PBS_O_WORKDIR}
#sample=$1
samtools=/ngs/Bioinf/soft/cellar/samtools/bin/samtools
ref=/ngs/Bioinf/Database/ref/hg19/seq/hg19.fa
bedtools=/ngs/Bioinf/soft/cellar/bedtools/bin
shome=/cgdata/guocq/script/2022-FeBY2
target=$shome/bed/test/FeBY2_20210902.sorted.hg19.bed
export PERL5LIB=~/perl5/lib/perl5

slopBed -i $target -g $ref.fai -b 80 |mergeBed > $target.200.bed
perl $shome/gc/get_GC_Refcnt.pl 200 $ref hg19 $target.200.bed 1 > FeBY2_2022.GC_REF.200_$run.xls
cut -f2,6 FeBY2_2022.GC_REF.200_$run.xls |awk '$2~/^[1-9]/ && $2>900' > FeBY2_2022.GC_REF.200.tsv

slopBed -i $target -g $ref.fai -b 180 |mergeBed > $target.300.bed
perl $shome/gc/get_GC_Refcnt.pl 300 $ref hg19 $target.300.bed 1 > FeBY2_2022.GC_REF.300_$run.xls
cut -f2,6 FeBY2_2022.GC_REF.300_$run.xls |awk '$2~/^[1-9]/ && $2>900' > FeBY2_2022.GC_REF.300.tsv