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

time $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/0hrep1/ugc_604_1_F3.csfasta  -N 20 -n 1 --local -o 10 -v 20% -h 20% -r 30% -w 150% -P -e -255 -f -255   >0hrep1-15mMm.out 2>0hrep1-15mMm.log
time $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% -P -e -255 -f -255   >0hrep2-15mMm.out 2>0hrep2-15mMm.log
time $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% -P -e -255 -f -255   >0hrep3-15mMm.out 2>0hrep3-15mMm.log
time $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/2hrep1/*.csfasta  -N 19 -n 1 --local -o 10 -v 20% -h 20% -r 30% -w 150% -P -e -255 -f -255   >2hrep1-15mMm.out 2>2hrep1-15mMm.log
time $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/2hrep2/*.csfasta  -N 20 -n 1 --local -o 10 -v 20% -h 20% -r 30% -w 150% -P -e -255 -f -255   >2hrep2-15mMm.out 2>2hrep2-15mMm.log
time $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/2hrep3/*.csfasta  -N 20 -n 1 --local -o 10 -v 20% -h 20% -r 30% -w 150% -P -e -255 -f -255   >2hrep3-15mMm.out 2>2hrep3-15mMm.log 
time $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% -P -e -255 -f -255   >6hrep1-15mMm.out 2>6hrep1-15mMm.log
time $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% -P -e -255 -f -255   >6hrep2-15mMm.out 2>6hrep2-15mMm.log
time $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/6hrep3/ugc_604_9_F3.csfasta  -N 20 -n 1 --local -o 10 -v 20% -h 20% -r 30% -w 150% -P -e -255 -f -255   >6hrep3-15mMm.out 2>6hrep3-15mMm.log
time $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% -P -e -255 -f -255   >IFN-15mMm.out 2>IFN-15mMm.log
time $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% -P -e -255 -f -255   >IGG-15mMm.out 2>IGG-15mMm.log
time $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% -P -e -255 -f -255   >IL4-15mMm.out 2>IL4-15mMm.log