export SHRIMP_FOLDER=/data/results/tools/align/SHRiMP_2_2_3


 $SHRIMP_FOLDER/bin/gmapper-cs -L /data/results/reference/mmu/mm9/shrimp/shrimp-15mMm/mm9-stranded-mRNA-cs /data/images/proton/DKlab/mr/parclip/raw/0hrep3/ugc_604_7_F3.csfasta  -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 - - >0hrep3-15mMm.bam 2>0hrep3-15mMm-bam.log
 $SHRIMP_FOLDER/bin/gmapper-cs -L /data/results/reference/mmu/mm9/shrimp/shrimp-15mMm/mm9-stranded-mRNA-cs /data/images/proton/DKlab/mr/parclip/raw/IL4/ugc_604_11_F3.csfasta    -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 - - >IL4-15mMm.bam 2>IL4-15mMm-bam.log
 $SHRIMP_FOLDER/bin/gmapper-cs -L /data/results/reference/mmu/mm9/shrimp/shrimp-15mMm/mm9-stranded-mRNA-cs /data/images/proton/DKlab/mr/parclip/raw/6hrep1/ugc_604_3_F3.csfasta  -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 - - >6hrep1-15mMm.bam 2>6hrep1-bam.log
 $SHRIMP_FOLDER/bin/gmapper-cs -L /data/results/reference/mmu/mm9/shrimp/shrimp-15mMm/mm9-stranded-mRNA-cs /data/images/proton/DKlab/mr/parclip/raw/6hrep2/ugc_604_6_F3.csfasta  -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 - - >6hrep2-15mMm.bam 2>6hrep2-bam.log
 $SHRIMP_FOLDER/bin/gmapper-cs -L /data/results/reference/mmu/mm9/shrimp/shrimp-15mMm/mm9-stranded-mRNA-cs /data/images/proton/DKlab/mr/parclip/raw/0hrep2/ugc_604_4_F3.csfasta  -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 - - >0hrep2-15mMm.bam 2>0hrep2-bam.log
 $SHRIMP_FOLDER/bin/gmapper-cs -L /data/results/reference/mmu/mm9/shrimp/shrimp-15mMm/mm9-stranded-mRNA-cs /data/images/proton/DKlab/mr/parclip/raw/IFN/ugc_604_10_F3.csfasta    -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 - - >IFN-15mMm.bam 2>IFN-bam.log
 $SHRIMP_FOLDER/bin/gmapper-cs -L /data/results/reference/mmu/mm9/shrimp/shrimp-15mMm/mm9-stranded-mRNA-cs /data/images/proton/DKlab/mr/parclip/raw/IGG/ugc_604_12_F3.csfasta    -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 - - >IGG-15mMm.bam 2>IGG-bam.log