export SHRIMP_FOLDER=/data/results/tools/align/SHRiMP_2_2_3
#shrimp/shrimp-15mMm/mm9-stranded mRNA-genomic/mm9-genomic
$SHRIMP_FOLDER/bin/gmapper-cs -L /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs  /data/images/proton/DKlab/mr/parclip/raw/2hrep1/*.csfasta  -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 - - >2hrep1-15mMm1kIntron.bam 2>2hrep1-15mMm1kIntron-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/2hrep2/*.csfasta  -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 - - >2hrep2-15mMm1kIntron.bam 2>2hrep2-15mMm1kIntron-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/2hrep3/*.csfasta  -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 - - >2hrep3-15mMm1kIntron.bam 2>2hrep3-15mMm1kIntron-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/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/mRNA-genomic-max-intron-15k/mm9-mRNA-introns1k-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/mRNA-genomic-max-intron-15k/mm9-mRNA-introns1k-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/mRNA-genomic-max-intron-15k/mm9-mRNA-introns1k-cs /data/images/proton/DKlab/mr/parclip/raw/6hrep3/ugc_604_9_F3.csfasta  -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 - - >6hrep3-15mMm1kIntron.bam 2>6hrep3-15mMm1kIntron-bam.log