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/IL4-q25-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 - - >IL4-15mMm.bam 2>IL4-15mMm-bam.log

$SHRIMP_FOLDER/bin/gmapper-cs -L /data/results/reference/mmu/mm9/mRNA-genomic-max-intron-15k/mm9-mRNA-introns1k-cs /data/images/proton/DKlab/mr/parclip/raw/IGG-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 - - >IGG-q20.bam 2>IGG-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/IL4-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 - - >IL4-q20.bam 2>IL4-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/0hrep1-q20-m15.fa  -N 11 -n 1 --local -o 10 -v 20% -h 20% -r 30% -w 150% -e -255 -f -255  | samtools view -Sb - | samtools sort -o - - >0hrep1-q20.bam 2>0hrep1-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/0hrep2-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 - - >0hrep2-q20.bam 2>0hrep2-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/0hrep3-q20-m15.fa  -N 11 -n 1 --local -o 10 -v 20% -h 20% -r 30% -w 150% -e -255 -f -255  | samtools view -Sb - | samtools sort -o - - >0hrep3-q20.bam 2>0hrep3-q20-bam.log