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run_pc_jamm.sh
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executable file
·68 lines (48 loc) · 2.11 KB
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NAME=$1
SET=$2
TOOL=$3
mkdir -p results_peaks/$TOOL results_peaks/$TOOL/$SET
mkdir -p log/pc log/pc/$TOOL
files=$(ls results_peaks/$TOOL/$SET/*/*.bed 2> /dev/null | wc -l)
if [ "$files" = "0" ]; then
echo "running peak calling tool: $TOOL with: $1 $2 $3" #$4 $5 $6 $7 $8 $9"
cd results_peaks/$TOOL/$SET/
LOG="../../../log/pc/$TOOL/$SET.log"
RESULTSDIR="../../../results_peaks/$TOOL/$SET"
mkdir s1 i1 s2 i2 r1 r2
bamToBed -i $4 > s1/S11.bed
bamToBed -i $5 > s1/S12.bed
bamToBed -i $6 > i1/IN1.bed
bamToBed -i $7 > s2/S21.bed
bamToBed -i $8 > s2/S22.bed
bamToBed -i $9 > i2/IN2.bed
#sharp
PCRUN=$RESULTSDIR"/sharp"
mkdir -p $PCRUN
bash /apps/JAMM-JAMMv1.0.7.6/JAMM.sh -s s1 -c i1 -g /ssd/references/THOR/mm10/chr19.chrom.size -o r1 -r peak >> $LOG 2>&1
cat r1/peaks/filtered.peaks.narrowPeak | cut -f1,2,3,7 > $PCRUN/s11_peaks.bed #chr start stop and score
cat r1/peaks/filtered.peaks.narrowPeak | cut -f1,2,3,7 > $PCRUN/s12_peaks.bed
#clean up
rm -rf r1/*
bash /apps/JAMM-JAMMv1.0.7.6/JAMM.sh -s s2 -c i2 -g /ssd/references/THOR/mm10/chr19.chrom.size -o r2 -r peak >> $LOG 2>&1
cat r2/peaks/filtered.peaks.narrowPeak | cut -f1,2,3,7 > $PCRUN/s21_peaks.bed
cat r2/peaks/filtered.peaks.narrowPeak | cut -f1,2,3,7 > $PCRUN/s22_peaks.bed
#clean up
rm -rf r2/*
#broad
PCRUN=$RESULTSDIR"/broad"
mkdir -p $PCRUN
bash /apps/JAMM-JAMMv1.0.7.6/JAMM.sh -s s1 -c i1 -g /ssd/references/THOR/mm10/chr19.chrom.size -o r1 -r window -b 1000 -w 1 >> $LOG 2>&1
cat r1/peaks/filtered.peaks.narrowPeak | cut -f1,2,3,7 > $PCRUN/s11_peaks.bed
cat r1/peaks/filtered.peaks.narrowPeak | cut -f1,2,3,7 > $PCRUN/s12_peaks.bed
#clean up
rm -rf r1/*
bash /apps/JAMM-JAMMv1.0.7.6/JAMM.sh -s s2 -c i2 -g /ssd/references/THOR/mm10/chr19.chrom.size -o r2 -r window -b 1000 -w 1 >> $LOG 2>&1
cat r2/peaks/filtered.peaks.narrowPeak | cut -f1,2,3,7 > $PCRUN/s21_peaks.bed
cat r2/peaks/filtered.peaks.narrowPeak | cut -f1,2,3,7 > $PCRUN/s22_peaks.bed
#clean up
rm -rf r2/*
rm -rf i1 i2 r1 r2 s1 s2
else
echo "results_peaks/$TOOL/$SET/bed already exists exiting..."
fi