python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py ChIPseq_Gcn4-GSM2278610/all.1x36mers.a.bam SAMstats-ChIPseq_Gcn4-GSM2278610.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 ChIPseq_Input-GSM2278611/all.1x36mers.a.bam SAMstats-ChIPseq_Input-GSM2278611.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 --- ChIPseq_Gcn4-GSM2278610/all.1x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes ChIPseq_Gcn4-GSM2278610/all.1x36mers.a.wig -notitle -RPM 
python ~/code/makewigglefromBAM-NH.py --- ChIPseq_Input-GSM2278611/all.1x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes ChIPseq_Input-GSM2278611/all.1x36mers.a.wig -notitle -RPM