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/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  | samtools view -Sb - | samtools sort -o - - >IFN-15mMm2.bam 2>IFN-15mMm2-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% -P -e -255 -f -255 >IFN-15mMm2.sam 2>IFN-15mMm2-bam.log2