export SHRIMP_FOLDER=/data/results/tools/align/SHRiMP_2_2_3
$SHRIMP_FOLDER/bin/gmapper-cs -L /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs /data/images/proton/DKlab/mr/parclip/raw/2hrep1-q20-m15.fa  -N 20 -n 1 --local -o 10 -v 20% -h 20% -r 30% -w 150% -e -255 -f -255  | samtools view -Sb - | samtools sort -o - - >2hrep1-q20.bam 2>2hrep1-q20-bam.log
 $SHRIMP_FOLDER/bin/gmapper-cs -L /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs /data/images/proton/DKlab/mr/parclip/raw/2hrep2-q20-m15.fa  -N 20 -n 1 --local -o 10 -v 20% -h 20% -r 30% -w 150% -e -255 -f -255  | samtools view -Sb - | samtools sort -o - - >2hrep2-q20.bam 2>2hrep2-q20-bam.log
 $SHRIMP_FOLDER/bin/gmapper-cs -L /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs /data/images/proton/DKlab/mr/parclip/raw/2hrep3-q20-m15.fa  -N 20 -n 1 --local -o 10 -v 20% -h 20% -r 30% -w 150% -e -255 -f -255  | samtools view -Sb - | samtools sort -o - - >2hrep3-q20.bam 2>2hrep3-q20-bam.log