./SeqTrimMap4Paralyzer2 -m 10 -l 18 -v 2 -p 10 -i -o IL4F-4p10  IL4filt7_T_F3.csfasta.coll  /data/results/reference/mmu/mm9/bowtie1/mm9c
./SeqTrimMap4Paralyzer2 -m 10 -l 18 -v 2 -p 10 -i -o IFNF-4p10  IFNfilt7_T_F3.csfasta.coll  /data/results/reference/mmu/mm9/bowtie1/mm9c

./SeqTrimMap4Paralyzer2 -m 10 -l 18 -v 2 -p 10 -i -o 6hrep1F-4p10  6hrep1filt7_T_F3.csfasta.coll  /data/results/reference/mmu/mm9/bowtie1/mm9c
./SeqTrimMap4Paralyzer2 -m 10 -l 18 -v 2 -p 10 -i -o 6hrep2F-4p10  6hrep2filt7_T_F3.csfasta.coll  /data/results/reference/mmu/mm9/bowtie1/mm9c
./SeqTrimMap4Paralyzer2 -m 10 -l 18 -v 2 -p 10 -i -o 6hrep3F-4p10  6hrep3filt7_T_F3.csfasta.coll  /data/results/reference/mmu/mm9/bowtie1/mm9c


/data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl /data/images/proton/DKlab/mr/parclip/raw/0hrep1F-4p10.bowtie > 0hrep1F-4p10.sam
/data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl /data/images/proton/DKlab/mr/parclip/raw/0hrep2F-4p10.bowtie > 0hrep2F-4p10.sam
#/data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl /data/images/proton/DKlab/mr/parclip/raw/0hrep3F-4p10.bowtie > 0hrep3F-4p10.sam

/data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl /data/images/proton/DKlab/mr/parclip/raw/2hrep1F-4p10.bowtie > 2hrep1F-4p10.sam
/data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl /data/images/proton/DKlab/mr/parclip/raw/2hrep2F-4p10.bowtie > 2hrep2F-4p10.sam
/data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl /data/images/proton/DKlab/mr/parclip/raw/2hrep3F-4p10.bowtie > 2hrep3F-4p10.sam
/data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl /data/images/proton/DKlab/mr/parclip/raw/6hrep1F-4p10.bowtie > 6hrep1F-4p10.sam
/data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl /data/images/proton/DKlab/mr/parclip/raw/6hrep2F-4p10.bowtie > 6hrep2F-4p10.sam
/data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl /data/images/proton/DKlab/mr/parclip/raw/6hrep3F-4p10.bowtie > 6hrep3F-4p10.sam

/data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl /data/images/proton/DKlab/mr/parclip/raw/IGGF-4p10.bowtie > IGGF-4p10.sam
/data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl /data/images/proton/DKlab/mr/parclip/raw/IFNF-4p10.bowtie > IFNF-4p10.sam
/data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl /data/images/proton/DKlab/mr/parclip/raw/IL4F-4p10.bowtie > IL4F-4p10.sam
source foo2.sh