python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py wildtype-MNase-0hr-rep1_B-GSM724109/alignments.36mers.a.bam SAMstats-wildtype-MNase-0hr-rep1_B-GSM724109.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py wildtype-MNase-3hr-rep1_B-GSM724110/alignments.36mers.a.bam SAMstats-wildtype-MNase-3hr-rep1_B-GSM724110.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py wildtype-MNase-0hr-rep1_C-GSM724111/alignments.36mers.a.bam SAMstats-wildtype-MNase-0hr-rep1_C-GSM724111.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py wildtype-MNase-3hr-rep1_C-GSM724112/alignments.36mers.a.bam SAMstats-wildtype-MNase-3hr-rep1_C-GSM724112.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired 
python ~/code/makewigglefromBAM-NH.py --- wildtype-MNase-0hr-rep1_B-GSM724109/alignments.36mers.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes wildtype-MNase-0hr-rep1_B-GSM724109/alignments.36mers.a.64bp_shift.wig -notitle -RPM  -shift 64 
python ~/code/makewigglefromBAM-NH.py --- wildtype-MNase-3hr-rep1_B-GSM724110/alignments.36mers.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes wildtype-MNase-3hr-rep1_B-GSM724110/alignments.36mers.a.64bp_shift.wig -notitle -RPM  -shift 64
python ~/code/makewigglefromBAM-NH.py --- wildtype-MNase-0hr-rep1_C-GSM724111/alignments.36mers.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes wildtype-MNase-0hr-rep1_C-GSM724111/alignments.36mers.a.64bp_shift.wig -notitle -RPM  -shift 64 
python ~/code/makewigglefromBAM-NH.py --- wildtype-MNase-3hr-rep1_C-GSM724112/alignments.36mers.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes wildtype-MNase-3hr-rep1_C-GSM724112/alignments.36mers.a.64bp_shift.wig -notitle -RPM  -shift 64