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/IFN-q20-m15.fa  -N 12 -n 1 --local -o 10 -v 20% -h 20% -r 30% -w 150% -e -255 -f -255  | samtools view -Sb - | samtools sort -o - - >IFN-q20.bam 2>IFN-q20-bam.log



$SHRIMP_FOLDER/bin/gmapper-cs -L /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs /data/images/proton/DKlab/mr/parclip/raw/6hrep1-q20-m15.fa  -N 12 -n 1 --local -o 10 -v 20% -h 20% -r 30% -w 150% -e -255 -f -255  | samtools view -Sb - | samtools sort -o - - >6hrep1-q20.bam 2>6hrep1-q20-bam.log
#$SHRIMP_FOLDER/bin/gmapper-cs -L /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs /data/images/proton/DKlab/mr/parclip/raw/6hrep2-q20-m15.fa  -N 12 -n 1 --local -o 10 -v 20% -h 20% -r 30% -w 150% -e -255 -f -255  | samtools view -Sb - | samtools sort -o - - >6hrep2-q20.bam 2>6hrep2-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/6hrep3-q20-m15.fa  -N 12 -n 1 --local -o 10 -v 20% -h 20% -r 30% -w 150% -e -255 -f -255  | samtools view -Sb - | samtools sort -o - - >6hrep3-q20.bam 2>6hrep3-q20-bam.log